Starting phenix.real_space_refine on Mon Apr 6 15:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu2_60887/04_2026/9iu2_60887.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu2_60887/04_2026/9iu2_60887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iu2_60887/04_2026/9iu2_60887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu2_60887/04_2026/9iu2_60887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu2_60887/04_2026/9iu2_60887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu2_60887/04_2026/9iu2_60887.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 196 5.49 5 S 60 5.16 5 C 11581 2.51 5 N 3618 2.21 5 O 4023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19482 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3871 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Conformer: "B" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} bond proxies already assigned to first conformer: 3938 Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1066 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1066 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "G1" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 39.091 160.743 78.879 1.00289.32 S ATOM 2447 SG CYS A 307 40.099 157.968 76.797 1.00289.25 S ATOM 2598 SG CYS A 326 42.088 158.675 79.158 1.00289.66 S ATOM 2670 SG CYS A 335 41.825 161.316 76.462 1.00290.81 S ATOM 6300 SG CYS B 304 72.950 34.998 121.883 1.00259.52 S ATOM 6318 SG CYS B 307 72.849 36.196 118.487 1.00258.98 S ATOM 6469 SG CYS B 326 70.061 36.086 119.927 1.00259.05 S ATOM 6541 SG CYS B 335 71.610 32.706 119.262 1.00261.17 S ATOM 10163 SG CYS C 304 78.327 124.672 16.729 1.00260.66 S ATOM 10181 SG CYS C 307 78.037 121.115 16.282 1.00258.84 S ATOM 10332 SG CYS C 326 80.170 121.953 18.440 1.00254.39 S ATOM 10404 SG CYS C 335 81.118 122.910 14.986 1.00254.41 S ATOM 14026 SG CYS D 304 59.508 25.383 41.460 1.00223.63 S ATOM 14044 SG CYS D 307 60.067 28.088 39.184 1.00222.44 S ATOM 14195 SG CYS D 326 57.221 28.128 40.485 1.00217.73 S ATOM 14267 SG CYS D 335 57.799 25.258 38.123 1.00219.72 S Time building chain proxies: 4.62, per 1000 atoms: 0.24 Number of scatterers: 19482 At special positions: 0 Unit cell: (121.11, 190.484, 158.737, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 60 16.00 P 196 15.00 O 4023 8.00 N 3618 7.00 C 11581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 806.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 307 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 304 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 326 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " 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 307 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 335 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 304 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 326 " Number of angles added : 24 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 49.7% alpha, 13.8% beta 96 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.619A 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 117 through 151 removed outlier: 3.891A pdb=" N VAL A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.135A 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: 3.794A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.526A pdb=" N GLN A 446 " --> pdb=" O TRP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'B' and resid 18 through 34 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.615A pdb=" N TRP B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 118 through 151 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 271 through 284 removed outlier: 4.083A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.850A pdb=" N VAL B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.526A pdb=" N GLN B 446 " --> pdb=" O TRP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.630A 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: 3.677A pdb=" N LEU C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Processing helix chain 'C' and resid 439 through 446 removed outlier: 3.522A pdb=" N GLN C 446 " --> pdb=" O TRP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 478 through 486 Processing helix chain 'D' and resid 17 through 34 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.635A 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 removed outlier: 3.527A pdb=" N GLN D 446 " --> pdb=" O TRP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 44 removed outlier: 7.503A pdb=" N VAL A 5 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 40 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 7 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU A 42 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU A 9 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU A 44 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG A 2 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 76 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.217A 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: 7.085A 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: 7.502A pdb=" N VAL B 5 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 40 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 7 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU B 42 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 9 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU B 44 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.232A 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: 7.086A 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: 7.523A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.219A 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: 7.094A 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: 7.484A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.223A 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: 7.117A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 251 hydrogen bonds 502 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 1.93 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: 3393 1.33 - 1.45: 6215 1.45 - 1.57: 10209 1.57 - 1.70: 389 1.70 - 1.82: 92 Bond restraints: 20298 Sorted by residual: bond pdb=" CA SER A 157 " pdb=" CB SER A 157 " ideal model delta sigma weight residual 1.530 1.450 0.081 1.69e-02 3.50e+03 2.27e+01 bond pdb=" CG HIS A 100 " pdb=" CD2 HIS A 100 " ideal model delta sigma weight residual 1.354 1.305 0.049 1.10e-02 8.26e+03 2.00e+01 bond pdb=" CA SER D 157 " pdb=" CB SER D 157 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.69e-02 3.50e+03 1.47e+01 bond pdb=" CA SER B 157 " pdb=" CB SER B 157 " ideal model delta sigma weight residual 1.530 1.469 0.061 1.69e-02 3.50e+03 1.32e+01 bond pdb=" C HIS C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.330 1.370 -0.040 1.22e-02 6.72e+03 1.07e+01 ... (remaining 20293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 27054 4.30 - 8.59: 1249 8.59 - 12.89: 51 12.89 - 17.19: 6 17.19 - 21.48: 2 Bond angle restraints: 28362 Sorted by residual: angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 82.52 21.48 1.50e+00 4.44e-01 2.05e+02 angle pdb=" O3' DG F 29 " pdb=" P DC F 30 " pdb=" O5' DC F 30 " ideal model delta sigma weight residual 104.00 86.34 17.66 1.50e+00 4.44e-01 1.39e+02 angle pdb=" O3' DG F 32 " pdb=" P DT F 33 " pdb=" O5' DT F 33 " ideal model delta sigma weight residual 104.00 87.63 16.37 1.50e+00 4.44e-01 1.19e+02 angle pdb=" O3' DT F 33 " pdb=" C3' DT F 33 " pdb=" C2' DT F 33 " ideal model delta sigma weight residual 111.50 97.89 13.61 1.50e+00 4.44e-01 8.23e+01 angle pdb=" O3' DG E 32 " pdb=" P DT E 33 " pdb=" O5' DT E 33 " ideal model delta sigma weight residual 104.00 90.48 13.52 1.50e+00 4.44e-01 8.12e+01 ... (remaining 28357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9422 17.92 - 35.84: 1272 35.84 - 53.77: 718 53.77 - 71.69: 184 71.69 - 89.61: 27 Dihedral angle restraints: 11623 sinusoidal: 6007 harmonic: 5616 Sorted by residual: dihedral pdb=" CA THR B 17 " pdb=" C THR B 17 " pdb=" N SER B 18 " pdb=" CA SER B 18 " ideal model delta harmonic sigma weight residual 180.00 143.77 36.23 0 5.00e+00 4.00e-02 5.25e+01 dihedral pdb=" CA LEU D 282 " pdb=" C LEU D 282 " pdb=" N VAL D 283 " pdb=" CA VAL D 283 " ideal model delta harmonic sigma weight residual -180.00 -148.13 -31.87 0 5.00e+00 4.00e-02 4.06e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N ALA A 15 " pdb=" CA ALA A 15 " ideal model delta harmonic sigma weight residual -180.00 -148.31 -31.69 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 11620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2610 0.128 - 0.256: 441 0.256 - 0.384: 45 0.384 - 0.512: 9 0.512 - 0.640: 4 Chirality restraints: 3109 Sorted by residual: chirality pdb=" P DT F 1 " pdb=" OP1 DT F 1 " pdb=" OP2 DT F 1 " pdb=" O5' DT F 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DGG1 1 " pdb=" OP1 DGG1 1 " pdb=" OP2 DGG1 1 " pdb=" O5' DGG1 1 " both_signs ideal model delta sigma weight residual True 2.35 2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 3106 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC E 30 " 0.163 2.00e-02 2.50e+03 7.44e-02 1.25e+02 pdb=" N1 DC E 30 " -0.088 2.00e-02 2.50e+03 pdb=" C2 DC E 30 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DC E 30 " -0.047 2.00e-02 2.50e+03 pdb=" N3 DC E 30 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DC E 30 " 0.028 2.00e-02 2.50e+03 pdb=" N4 DC E 30 " 0.070 2.00e-02 2.50e+03 pdb=" C5 DC E 30 " -0.036 2.00e-02 2.50e+03 pdb=" C6 DC E 30 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 32 " 0.092 2.00e-02 2.50e+03 4.37e-02 5.72e+01 pdb=" N9 DG E 32 " -0.038 2.00e-02 2.50e+03 pdb=" C8 DG E 32 " -0.022 2.00e-02 2.50e+03 pdb=" N7 DG E 32 " -0.061 2.00e-02 2.50e+03 pdb=" C5 DG E 32 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG E 32 " 0.050 2.00e-02 2.50e+03 pdb=" O6 DG E 32 " 0.038 2.00e-02 2.50e+03 pdb=" N1 DG E 32 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DG E 32 " -0.062 2.00e-02 2.50e+03 pdb=" N2 DG E 32 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG E 32 " -0.018 2.00e-02 2.50e+03 pdb=" C4 DG E 32 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCH1 27 " -0.097 2.00e-02 2.50e+03 4.56e-02 4.69e+01 pdb=" N1 DCH1 27 " 0.066 2.00e-02 2.50e+03 pdb=" C2 DCH1 27 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DCH1 27 " 0.035 2.00e-02 2.50e+03 pdb=" N3 DCH1 27 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DCH1 27 " -0.020 2.00e-02 2.50e+03 pdb=" N4 DCH1 27 " -0.026 2.00e-02 2.50e+03 pdb=" C5 DCH1 27 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DCH1 27 " 0.049 2.00e-02 2.50e+03 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 3 2.25 - 2.91: 6406 2.91 - 3.58: 28613 3.58 - 4.24: 48167 4.24 - 4.90: 77399 Nonbonded interactions: 160588 Sorted by model distance: nonbonded pdb=" OG SER C 10 " pdb=" P DCH1 25 " model vdw 1.592 3.400 nonbonded pdb=" OG SER D 10 " pdb=" P DCG2 25 " model vdw 1.596 3.400 nonbonded pdb=" NH1 ARG B 58 " pdb=" O LEU B 83 " model vdw 2.248 3.120 nonbonded pdb=" O5' DTH2 24 " pdb=" O4' DTH2 24 " model vdw 2.260 2.432 nonbonded pdb=" NH1 ARG A 58 " pdb=" O LEU A 83 " model vdw 2.265 3.120 ... (remaining 160583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'B' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'C' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'D' and (resid 1 through 141 or resid 143 through 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.130 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 20314 Z= 0.661 Angle : 2.007 21.484 28386 Z= 1.266 Chirality : 0.098 0.640 3109 Planarity : 0.009 0.089 3022 Dihedral : 20.879 89.609 7989 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % Rotamer: Outliers : 4.42 % Allowed : 6.67 % Favored : 88.91 % Cbeta Deviations : 1.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.04 (0.17), residues: 1937 helix: 0.22 (0.14), residues: 923 sheet: 0.01 (0.28), residues: 285 loop : 0.02 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.006 ARG B 2 TYR 0.030 0.007 TYR A 482 PHE 0.048 0.006 PHE A 112 TRP 0.055 0.007 TRP D 35 HIS 0.022 0.004 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.01085 (20298) covalent geometry : angle 1.98668 (28362) hydrogen bonds : bond 0.14866 ( 1060) hydrogen bonds : angle 5.75735 ( 2790) metal coordination : bond 0.12751 ( 16) metal coordination : angle 9.93878 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 489 time to evaluate : 0.540 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 1 MET cc_start: 0.7347 (mmm) cc_final: 0.7106 (mmm) REVERT: A 24 GLU cc_start: 0.8926 (tt0) cc_final: 0.8621 (tt0) REVERT: A 28 GLN cc_start: 0.8928 (tt0) cc_final: 0.8593 (tt0) REVERT: A 33 ARG cc_start: 0.7955 (mmt90) cc_final: 0.7502 (mmt90) REVERT: A 73 ASP cc_start: 0.6524 (m-30) cc_final: 0.6215 (m-30) REVERT: A 86 SER cc_start: 0.6473 (t) cc_final: 0.5758 (p) REVERT: A 98 GLU cc_start: 0.7666 (tp30) cc_final: 0.7219 (tp30) REVERT: A 100 HIS cc_start: 0.7180 (m-70) cc_final: 0.6763 (m170) REVERT: A 111 HIS cc_start: 0.6922 (p90) cc_final: 0.6612 (p90) REVERT: A 137 ILE cc_start: 0.7656 (mt) cc_final: 0.7247 (tt) REVERT: A 140 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7392 (tmm-80) REVERT: A 147 PHE cc_start: 0.7988 (t80) cc_final: 0.7747 (t80) REVERT: A 153 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8070 (mttp) REVERT: A 169 ASP cc_start: 0.7394 (t0) cc_final: 0.7169 (t0) REVERT: A 196 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6407 (mt-10) REVERT: A 200 LEU cc_start: 0.8126 (mt) cc_final: 0.7805 (mt) REVERT: A 239 MET cc_start: 0.7530 (mmm) cc_final: 0.7327 (mmm) REVERT: A 263 LEU cc_start: 0.7511 (tp) cc_final: 0.7066 (tt) REVERT: A 274 GLN cc_start: 0.6944 (mt0) cc_final: 0.6681 (mt0) REVERT: A 376 GLU cc_start: 0.8435 (tt0) cc_final: 0.7722 (tt0) REVERT: A 407 ASP cc_start: 0.8236 (m-30) cc_final: 0.7944 (p0) REVERT: A 409 ARG cc_start: 0.8796 (ttp-170) cc_final: 0.8584 (ptm160) REVERT: A 455 LEU cc_start: 0.8582 (mt) cc_final: 0.7994 (mp) REVERT: A 458 MET cc_start: 0.7945 (mmm) cc_final: 0.6979 (tmm) REVERT: A 481 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: B 1 MET cc_start: 0.6452 (mmm) cc_final: 0.6180 (mmm) REVERT: B 24 GLU cc_start: 0.7386 (tt0) cc_final: 0.6996 (tt0) REVERT: B 69 GLU cc_start: 0.5235 (OUTLIER) cc_final: 0.4798 (mp0) REVERT: B 79 ARG cc_start: 0.7052 (mtp85) cc_final: 0.6721 (mtm110) REVERT: B 80 VAL cc_start: 0.7254 (t) cc_final: 0.7054 (m) REVERT: B 81 ASP cc_start: 0.8048 (p0) cc_final: 0.7708 (p0) REVERT: B 85 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7451 (mtt90) REVERT: B 133 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6997 (mt-10) REVERT: B 135 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 138 LYS cc_start: 0.7643 (mttt) cc_final: 0.7442 (mttp) REVERT: B 139 GLU cc_start: 0.7901 (tt0) cc_final: 0.7610 (tt0) REVERT: B 141 ASN cc_start: 0.8060 (m-40) cc_final: 0.7747 (m-40) REVERT: B 153 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8265 (mttm) REVERT: B 155 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7501 (ptt-90) REVERT: B 204 ASP cc_start: 0.7331 (t70) cc_final: 0.6977 (t0) REVERT: B 242 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 257 ASP cc_start: 0.7098 (t70) cc_final: 0.6714 (t70) REVERT: B 267 GLU cc_start: 0.6649 (tt0) cc_final: 0.6388 (tt0) REVERT: B 273 GLU cc_start: 0.7722 (tt0) cc_final: 0.7094 (mm-30) REVERT: B 342 MET cc_start: 0.3949 (ttp) cc_final: 0.3662 (ttp) REVERT: B 348 PHE cc_start: 0.8547 (t80) cc_final: 0.8327 (t80) REVERT: B 376 GLU cc_start: 0.8116 (tt0) cc_final: 0.7310 (tt0) REVERT: B 443 TRP cc_start: 0.8010 (t-100) cc_final: 0.7477 (t-100) REVERT: B 458 MET cc_start: 0.7665 (mmt) cc_final: 0.7458 (mmp) REVERT: B 480 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7250 (tp40) REVERT: C 46 VAL cc_start: 0.7863 (t) cc_final: 0.7518 (p) REVERT: C 51 ASP cc_start: 0.7618 (t0) cc_final: 0.7276 (t0) REVERT: C 54 ASP cc_start: 0.6707 (t0) cc_final: 0.6094 (t0) REVERT: C 57 ARG cc_start: 0.6946 (mmt90) cc_final: 0.6694 (mmt90) REVERT: C 73 ASP cc_start: 0.7296 (m-30) cc_final: 0.6765 (m-30) REVERT: C 79 ARG cc_start: 0.7075 (mtp85) cc_final: 0.6789 (mtp85) REVERT: C 92 GLN cc_start: 0.7333 (mt0) cc_final: 0.6973 (mt0) REVERT: C 109 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6437 (mt-10) REVERT: C 113 ASP cc_start: 0.7604 (t0) cc_final: 0.7204 (t0) REVERT: C 118 PHE cc_start: 0.7438 (p90) cc_final: 0.7165 (p90) REVERT: C 135 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7191 (mp0) REVERT: C 147 PHE cc_start: 0.7945 (t80) cc_final: 0.7740 (t80) REVERT: C 163 TYR cc_start: 0.7341 (m-80) cc_final: 0.6982 (m-80) REVERT: C 186 GLU cc_start: 0.7921 (tp30) cc_final: 0.7254 (tp30) REVERT: C 199 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6360 (p-80) REVERT: C 203 HIS cc_start: 0.7910 (t70) cc_final: 0.6993 (t70) REVERT: C 204 ASP cc_start: 0.7525 (m-30) cc_final: 0.7219 (m-30) REVERT: C 207 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7638 (mpp80) REVERT: C 208 ARG cc_start: 0.8434 (mpp80) cc_final: 0.7742 (mtt180) REVERT: C 220 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7452 (tt) REVERT: C 229 GLU cc_start: 0.7507 (pt0) cc_final: 0.7303 (pt0) REVERT: C 279 ARG cc_start: 0.7034 (mtt180) cc_final: 0.6569 (mtt180) REVERT: C 314 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.5064 (p90) REVERT: C 329 MET cc_start: 0.7978 (ttm) cc_final: 0.7589 (ttm) REVERT: C 339 THR cc_start: 0.7371 (p) cc_final: 0.7168 (p) REVERT: C 345 TRP cc_start: 0.6922 (m100) cc_final: 0.6372 (m100) REVERT: D 27 GLN cc_start: 0.7078 (mt0) cc_final: 0.6579 (mm110) REVERT: D 28 GLN cc_start: 0.6766 (tm-30) cc_final: 0.6548 (tm-30) REVERT: D 79 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7561 (mtp85) REVERT: D 135 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7345 (mm-30) REVERT: D 153 LYS cc_start: 0.8411 (mttt) cc_final: 0.8193 (mttt) REVERT: D 164 LEU cc_start: 0.6745 (tp) cc_final: 0.6502 (mt) REVERT: D 166 THR cc_start: 0.6741 (OUTLIER) cc_final: 0.6393 (p) REVERT: D 173 ARG cc_start: 0.7332 (ttm110) cc_final: 0.6860 (mtp180) REVERT: D 182 GLU cc_start: 0.7639 (tt0) cc_final: 0.6900 (tm-30) REVERT: D 186 GLU cc_start: 0.7842 (tt0) cc_final: 0.7633 (tt0) REVERT: D 193 ASP cc_start: 0.7545 (m-30) cc_final: 0.7309 (m-30) REVERT: D 211 LEU cc_start: 0.7290 (mp) cc_final: 0.7033 (mt) REVERT: D 224 GLU cc_start: 0.7602 (tp30) cc_final: 0.7025 (tp30) REVERT: D 229 GLU cc_start: 0.7704 (pt0) cc_final: 0.7443 (pt0) REVERT: D 242 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6567 (mt-10) REVERT: D 247 TYR cc_start: 0.7853 (m-10) cc_final: 0.7329 (m-10) REVERT: D 265 ARG cc_start: 0.7129 (ptt180) cc_final: 0.6748 (ptt90) REVERT: D 313 LYS cc_start: 0.7240 (ttpp) cc_final: 0.6318 (ttpp) REVERT: D 334 HIS cc_start: 0.7073 (p90) cc_final: 0.6775 (p-80) REVERT: D 464 PHE cc_start: 0.5841 (p90) cc_final: 0.5065 (p90) outliers start: 71 outliers final: 22 residues processed: 532 average time/residue: 0.1734 time to fit residues: 131.1329 Evaluate side-chains 460 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 429 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 413 LEU 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 74 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 352 GLN 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 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 195 HIS B 22 GLN B 89 HIS B 92 GLN B 274 GLN C 27 GLN C 92 GLN C 100 HIS C 111 HIS C 180 GLN C 334 HIS C 480 GLN D 22 GLN D 91 GLN D 146 HIS D 189 HIS ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 452 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132055 restraints weight = 38418.199| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.70 r_work: 0.3376 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20314 Z= 0.162 Angle : 0.585 10.588 28386 Z= 0.324 Chirality : 0.038 0.196 3109 Planarity : 0.005 0.048 3022 Dihedral : 22.922 85.637 4343 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.18 % Allowed : 13.33 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1937 helix: 2.60 (0.16), residues: 916 sheet: 0.03 (0.27), residues: 303 loop : 0.88 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 58 TYR 0.012 0.001 TYR C 154 PHE 0.024 0.001 PHE A 348 TRP 0.013 0.001 TRP B 230 HIS 0.005 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00346 (20298) covalent geometry : angle 0.57795 (28362) hydrogen bonds : bond 0.04098 ( 1060) hydrogen bonds : angle 3.64462 ( 2790) metal coordination : bond 0.00444 ( 16) metal coordination : angle 3.11455 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 415 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6398 (mmm) cc_final: 0.6160 (mmm) REVERT: A 28 GLN cc_start: 0.8528 (tt0) cc_final: 0.8275 (tt0) REVERT: A 69 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6498 (mp0) REVERT: A 73 ASP cc_start: 0.6318 (m-30) cc_final: 0.6085 (m-30) REVERT: A 82 ARG cc_start: 0.7785 (mmt180) cc_final: 0.6965 (mmp80) REVERT: A 84 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7612 (m) REVERT: A 86 SER cc_start: 0.8325 (t) cc_final: 0.7547 (p) REVERT: A 98 GLU cc_start: 0.7298 (tp30) cc_final: 0.6882 (tp30) REVERT: A 100 HIS cc_start: 0.7974 (m170) cc_final: 0.7667 (m170) REVERT: A 137 ILE cc_start: 0.8641 (mt) cc_final: 0.8360 (tt) REVERT: A 147 PHE cc_start: 0.8682 (t80) cc_final: 0.8408 (t80) REVERT: A 192 VAL cc_start: 0.7684 (t) cc_final: 0.7357 (p) REVERT: A 200 LEU cc_start: 0.8203 (mt) cc_final: 0.7990 (mt) REVERT: A 203 HIS cc_start: 0.7652 (t-90) cc_final: 0.7201 (t-90) REVERT: A 342 MET cc_start: 0.5102 (ttp) cc_final: 0.4841 (mtp) REVERT: A 376 GLU cc_start: 0.8398 (tt0) cc_final: 0.7994 (tt0) REVERT: A 383 GLU cc_start: 0.8901 (tt0) cc_final: 0.8382 (tt0) REVERT: A 409 ARG cc_start: 0.8670 (ttp-170) cc_final: 0.8364 (ptm160) REVERT: A 418 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7464 (mm-30) REVERT: A 421 GLU cc_start: 0.5589 (mt-10) cc_final: 0.5080 (mt-10) REVERT: A 455 LEU cc_start: 0.8886 (mt) cc_final: 0.8346 (mm) REVERT: A 458 MET cc_start: 0.7900 (mmm) cc_final: 0.7329 (tmm) REVERT: A 481 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: B 1 MET cc_start: 0.7322 (mmm) cc_final: 0.7081 (mmm) REVERT: B 24 GLU cc_start: 0.7477 (tt0) cc_final: 0.7066 (tt0) REVERT: B 79 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7409 (mtm110) REVERT: B 81 ASP cc_start: 0.8435 (p0) cc_final: 0.8104 (p0) REVERT: B 133 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 135 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 141 ASN cc_start: 0.8645 (m-40) cc_final: 0.8311 (m-40) REVERT: B 143 SER cc_start: 0.8728 (t) cc_final: 0.8482 (m) REVERT: B 155 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8036 (ppt170) REVERT: B 204 ASP cc_start: 0.7951 (t70) cc_final: 0.7691 (t0) REVERT: B 342 MET cc_start: 0.5157 (ttp) cc_final: 0.4674 (ttp) REVERT: B 348 PHE cc_start: 0.8536 (t80) cc_final: 0.8228 (t80) REVERT: B 419 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 456 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8216 (mmm-85) REVERT: B 458 MET cc_start: 0.8300 (mmt) cc_final: 0.8016 (mmm) REVERT: C 10 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.5477 (t) REVERT: C 11 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7430 (ttp-170) REVERT: C 21 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7405 (tpp80) REVERT: C 24 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 46 VAL cc_start: 0.8440 (t) cc_final: 0.8196 (p) REVERT: C 54 ASP cc_start: 0.8068 (t0) cc_final: 0.7825 (t70) REVERT: C 69 GLU cc_start: 0.8303 (mp0) cc_final: 0.7612 (mm-30) REVERT: C 73 ASP cc_start: 0.7083 (m-30) cc_final: 0.6864 (m-30) REVERT: C 81 ASP cc_start: 0.7940 (p0) cc_final: 0.7707 (p0) REVERT: C 88 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7374 (mmm160) REVERT: C 91 GLN cc_start: 0.8428 (mt0) cc_final: 0.7924 (mt0) REVERT: C 92 GLN cc_start: 0.8020 (mt0) cc_final: 0.7600 (mt0) REVERT: C 118 PHE cc_start: 0.7582 (p90) cc_final: 0.7210 (p90) REVERT: C 140 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (mpt-90) REVERT: C 163 TYR cc_start: 0.8448 (m-80) cc_final: 0.8153 (m-80) REVERT: C 186 GLU cc_start: 0.8080 (tp30) cc_final: 0.7684 (tm-30) REVERT: C 199 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6579 (p-80) REVERT: C 203 HIS cc_start: 0.7872 (t70) cc_final: 0.7660 (t70) REVERT: C 208 ARG cc_start: 0.8574 (mpp80) cc_final: 0.8305 (mtm-85) REVERT: C 220 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8474 (tp) REVERT: C 242 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 267 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7722 (mm-30) REVERT: C 314 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6955 (p90) REVERT: C 325 ARG cc_start: 0.6421 (ttp-170) cc_final: 0.6006 (tmm-80) REVERT: C 339 THR cc_start: 0.7861 (p) cc_final: 0.7026 (t) REVERT: C 342 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.3962 (mmm) REVERT: C 345 TRP cc_start: 0.7710 (m100) cc_final: 0.7359 (m100) REVERT: C 348 PHE cc_start: 0.6802 (t80) cc_final: 0.6486 (t80) REVERT: D 24 GLU cc_start: 0.7740 (tt0) cc_final: 0.7358 (tt0) REVERT: D 27 GLN cc_start: 0.8136 (mt0) cc_final: 0.7831 (mm110) REVERT: D 28 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7379 (tm-30) REVERT: D 78 TYR cc_start: 0.8552 (t80) cc_final: 0.8272 (t80) REVERT: D 154 TYR cc_start: 0.8585 (t80) cc_final: 0.8015 (t80) REVERT: D 173 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7691 (mtp180) REVERT: D 182 GLU cc_start: 0.7040 (tt0) cc_final: 0.6563 (tm-30) REVERT: D 186 GLU cc_start: 0.7901 (tt0) cc_final: 0.7640 (tt0) REVERT: D 204 ASP cc_start: 0.7845 (t70) cc_final: 0.7476 (t0) REVERT: D 211 LEU cc_start: 0.8004 (mp) cc_final: 0.7662 (mt) REVERT: D 219 GLN cc_start: 0.7659 (tp-100) cc_final: 0.7325 (tt0) REVERT: D 226 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7947 (mm110) REVERT: D 265 ARG cc_start: 0.8229 (ptt180) cc_final: 0.7961 (ptt180) REVERT: D 309 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7054 (mm-30) REVERT: D 313 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7326 (ttpp) REVERT: D 329 MET cc_start: 0.7492 (tpp) cc_final: 0.6738 (tpp) REVERT: D 464 PHE cc_start: 0.6344 (p90) cc_final: 0.5982 (p90) outliers start: 51 outliers final: 25 residues processed: 445 average time/residue: 0.1713 time to fit residues: 109.5776 Evaluate side-chains 430 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 396 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 206 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 148 ASN A 189 HIS A 219 GLN A 334 HIS A 352 GLN B 100 HIS B 199 HIS B 274 GLN B 446 GLN D 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.178560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127373 restraints weight = 34356.838| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.53 r_work: 0.3302 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20314 Z= 0.272 Angle : 0.616 8.568 28386 Z= 0.342 Chirality : 0.042 0.221 3109 Planarity : 0.005 0.044 3022 Dihedral : 22.803 85.866 4303 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.05 % Allowed : 15.08 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.19), residues: 1937 helix: 2.48 (0.16), residues: 913 sheet: 0.12 (0.29), residues: 303 loop : 0.85 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 167 TYR 0.018 0.002 TYR B 154 PHE 0.020 0.002 PHE C 118 TRP 0.019 0.002 TRP A 35 HIS 0.028 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00602 (20298) covalent geometry : angle 0.60729 (28362) hydrogen bonds : bond 0.04507 ( 1060) hydrogen bonds : angle 3.68958 ( 2790) metal coordination : bond 0.00740 ( 16) metal coordination : angle 3.51987 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 414 time to evaluate : 0.509 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 28 GLN cc_start: 0.8504 (tt0) cc_final: 0.8250 (tt0) REVERT: A 64 TRP cc_start: 0.8254 (m-90) cc_final: 0.8040 (m-10) REVERT: A 69 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6535 (mp0) REVERT: A 82 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7454 (mmp80) REVERT: A 87 ILE cc_start: 0.8072 (mm) cc_final: 0.7730 (tp) REVERT: A 98 GLU cc_start: 0.7362 (tp30) cc_final: 0.6942 (tp30) REVERT: A 100 HIS cc_start: 0.7998 (m170) cc_final: 0.7627 (m170) REVERT: A 137 ILE cc_start: 0.8490 (mt) cc_final: 0.8251 (tt) REVERT: A 147 PHE cc_start: 0.8607 (t80) cc_final: 0.8376 (t80) REVERT: A 200 LEU cc_start: 0.8229 (mt) cc_final: 0.7890 (mm) REVERT: A 203 HIS cc_start: 0.7735 (t-90) cc_final: 0.7280 (t-90) REVERT: A 220 LEU cc_start: 0.8372 (mt) cc_final: 0.8057 (tt) REVERT: A 249 THR cc_start: 0.9091 (m) cc_final: 0.8855 (m) REVERT: A 376 GLU cc_start: 0.8462 (tt0) cc_final: 0.8193 (tt0) REVERT: A 383 GLU cc_start: 0.8913 (tt0) cc_final: 0.8493 (tt0) REVERT: A 409 ARG cc_start: 0.8716 (ttp-170) cc_final: 0.8430 (ptm160) REVERT: A 455 LEU cc_start: 0.8963 (mt) cc_final: 0.8299 (mm) REVERT: A 458 MET cc_start: 0.8100 (mmm) cc_final: 0.7504 (tmm) REVERT: A 481 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: B 79 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7269 (mtm180) REVERT: B 133 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 135 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 141 ASN cc_start: 0.8573 (m-40) cc_final: 0.8189 (m-40) REVERT: B 143 SER cc_start: 0.8691 (t) cc_final: 0.8391 (m) REVERT: B 155 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8135 (ppt170) REVERT: B 204 ASP cc_start: 0.7979 (t70) cc_final: 0.7752 (t0) REVERT: B 342 MET cc_start: 0.4922 (ttp) cc_final: 0.4500 (ttp) REVERT: B 348 PHE cc_start: 0.8703 (t80) cc_final: 0.8470 (t80) REVERT: B 371 SER cc_start: 0.8448 (t) cc_final: 0.8200 (p) REVERT: B 458 MET cc_start: 0.8264 (mmt) cc_final: 0.7783 (mmp) REVERT: C 10 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.6271 (t) REVERT: C 21 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7467 (tpp80) REVERT: C 24 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 46 VAL cc_start: 0.8596 (t) cc_final: 0.8390 (p) REVERT: C 54 ASP cc_start: 0.8219 (t0) cc_final: 0.7899 (t0) REVERT: C 56 LYS cc_start: 0.7937 (tppp) cc_final: 0.7683 (tppp) REVERT: C 57 ARG cc_start: 0.7506 (mmt90) cc_final: 0.7157 (mmt90) REVERT: C 73 ASP cc_start: 0.7278 (m-30) cc_final: 0.7016 (m-30) REVERT: C 92 GLN cc_start: 0.8190 (mt0) cc_final: 0.7961 (mt0) REVERT: C 99 ASP cc_start: 0.7162 (m-30) cc_final: 0.6874 (m-30) REVERT: C 113 ASP cc_start: 0.8318 (t0) cc_final: 0.8073 (t0) REVERT: C 163 TYR cc_start: 0.8754 (m-80) cc_final: 0.8374 (m-80) REVERT: C 177 ASP cc_start: 0.7311 (t0) cc_final: 0.7099 (t0) REVERT: C 186 GLU cc_start: 0.8107 (tp30) cc_final: 0.7569 (tp30) REVERT: C 203 HIS cc_start: 0.7863 (t70) cc_final: 0.7519 (t70) REVERT: C 208 ARG cc_start: 0.8577 (mpp80) cc_final: 0.7801 (mpp80) REVERT: C 240 ILE cc_start: 0.8235 (mm) cc_final: 0.8021 (tt) REVERT: C 242 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7566 (mt-10) REVERT: C 267 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 300 ARG cc_start: 0.8322 (mmt180) cc_final: 0.7671 (tpp-160) REVERT: C 303 PHE cc_start: 0.7234 (m-80) cc_final: 0.6404 (m-80) REVERT: C 309 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6790 (mp0) REVERT: C 314 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6685 (p90) REVERT: C 342 MET cc_start: 0.4686 (OUTLIER) cc_final: 0.3937 (mmm) REVERT: C 348 PHE cc_start: 0.7065 (t80) cc_final: 0.6699 (t80) REVERT: C 433 ARG cc_start: 0.7177 (tpp-160) cc_final: 0.6373 (mmt-90) REVERT: C 459 ASN cc_start: 0.8457 (m-40) cc_final: 0.8069 (m110) REVERT: C 461 ARG cc_start: 0.6958 (mtm110) cc_final: 0.6372 (tpp80) REVERT: D 27 GLN cc_start: 0.8129 (mt0) cc_final: 0.7888 (mm110) REVERT: D 28 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7263 (tm-30) REVERT: D 32 GLN cc_start: 0.7907 (tp40) cc_final: 0.7670 (tp40) REVERT: D 78 TYR cc_start: 0.8551 (t80) cc_final: 0.8231 (t80) REVERT: D 113 ASP cc_start: 0.7627 (p0) cc_final: 0.7359 (p0) REVERT: D 138 LYS cc_start: 0.8666 (mttt) cc_final: 0.8423 (mttp) REVERT: D 154 TYR cc_start: 0.8529 (t80) cc_final: 0.8041 (t80) REVERT: D 182 GLU cc_start: 0.7283 (tt0) cc_final: 0.6714 (tm-30) REVERT: D 186 GLU cc_start: 0.7936 (tt0) cc_final: 0.7689 (tt0) REVERT: D 204 ASP cc_start: 0.8029 (t70) cc_final: 0.7669 (t0) REVERT: D 211 LEU cc_start: 0.8367 (mp) cc_final: 0.8018 (mt) REVERT: D 219 GLN cc_start: 0.7665 (tp-100) cc_final: 0.7346 (tt0) REVERT: D 247 TYR cc_start: 0.8434 (m-10) cc_final: 0.8196 (m-10) REVERT: D 309 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7296 (mm-30) REVERT: D 329 MET cc_start: 0.7894 (tpp) cc_final: 0.7558 (tpp) REVERT: D 464 PHE cc_start: 0.6420 (p90) cc_final: 0.6140 (p90) outliers start: 65 outliers final: 44 residues processed: 447 average time/residue: 0.1772 time to fit residues: 113.2331 Evaluate side-chains 453 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 404 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 76 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 274 GLN B 91 GLN B 199 HIS C 27 GLN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 111 HIS D 226 GLN ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.186247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135931 restraints weight = 44565.787| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.81 r_work: 0.3267 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20314 Z= 0.260 Angle : 0.593 8.076 28386 Z= 0.328 Chirality : 0.041 0.181 3109 Planarity : 0.005 0.044 3022 Dihedral : 22.679 88.129 4290 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.60 % Favored : 98.35 % Rotamer: Outliers : 4.30 % Allowed : 15.70 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 1937 helix: 2.34 (0.16), residues: 914 sheet: 0.10 (0.29), residues: 301 loop : 0.76 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 272 TYR 0.017 0.002 TYR D 188 PHE 0.030 0.002 PHE C 118 TRP 0.017 0.001 TRP D 96 HIS 0.011 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00576 (20298) covalent geometry : angle 0.58433 (28362) hydrogen bonds : bond 0.04141 ( 1060) hydrogen bonds : angle 3.63498 ( 2790) metal coordination : bond 0.00659 ( 16) metal coordination : angle 3.47526 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 413 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7898 (mt0) cc_final: 0.7533 (mt0) REVERT: A 28 GLN cc_start: 0.8490 (tt0) cc_final: 0.8235 (tt0) REVERT: A 69 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6647 (mp0) REVERT: A 82 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7399 (mmp80) REVERT: A 87 ILE cc_start: 0.8110 (mm) cc_final: 0.7803 (tp) REVERT: A 98 GLU cc_start: 0.7378 (tp30) cc_final: 0.6909 (tp30) REVERT: A 100 HIS cc_start: 0.8022 (m170) cc_final: 0.7706 (m170) REVERT: A 137 ILE cc_start: 0.8577 (mt) cc_final: 0.8307 (tt) REVERT: A 182 GLU cc_start: 0.7393 (tt0) cc_final: 0.7125 (tt0) REVERT: A 200 LEU cc_start: 0.8225 (mt) cc_final: 0.7762 (mm) REVERT: A 203 HIS cc_start: 0.7791 (t-90) cc_final: 0.7313 (t-90) REVERT: A 219 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7340 (mm-40) REVERT: A 220 LEU cc_start: 0.8399 (mt) cc_final: 0.8147 (tp) REVERT: A 376 GLU cc_start: 0.8470 (tt0) cc_final: 0.8211 (tt0) REVERT: A 383 GLU cc_start: 0.8919 (tt0) cc_final: 0.8536 (tt0) REVERT: A 407 ASP cc_start: 0.8141 (m-30) cc_final: 0.7851 (m-30) REVERT: A 409 ARG cc_start: 0.8712 (ttp-170) cc_final: 0.8392 (ptm160) REVERT: A 455 LEU cc_start: 0.9000 (mt) cc_final: 0.8344 (mm) REVERT: A 456 ARG cc_start: 0.8514 (mtp180) cc_final: 0.7669 (mtp180) REVERT: A 458 MET cc_start: 0.8113 (mmm) cc_final: 0.7580 (tmm) REVERT: A 481 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: B 79 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7295 (mtm180) REVERT: B 133 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 135 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 141 ASN cc_start: 0.8558 (m-40) cc_final: 0.8188 (m-40) REVERT: B 143 SER cc_start: 0.8673 (t) cc_final: 0.8334 (m) REVERT: B 155 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8088 (ppt170) REVERT: B 204 ASP cc_start: 0.7995 (t70) cc_final: 0.7758 (t0) REVERT: B 284 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8068 (mtmm) REVERT: B 342 MET cc_start: 0.4945 (ttp) cc_final: 0.4536 (ttp) REVERT: B 345 TRP cc_start: 0.6958 (m100) cc_final: 0.6754 (m100) REVERT: B 371 SER cc_start: 0.8483 (t) cc_final: 0.8251 (p) REVERT: B 443 TRP cc_start: 0.7809 (t-100) cc_final: 0.7304 (t-100) REVERT: B 456 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8250 (mmm-85) REVERT: B 458 MET cc_start: 0.8284 (mmt) cc_final: 0.7821 (mmp) REVERT: C 10 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7473 (m) REVERT: C 21 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7510 (tpp80) REVERT: C 24 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 46 VAL cc_start: 0.8633 (t) cc_final: 0.8396 (p) REVERT: C 54 ASP cc_start: 0.8178 (t0) cc_final: 0.7805 (t0) REVERT: C 56 LYS cc_start: 0.7920 (tppp) cc_final: 0.7654 (tppp) REVERT: C 57 ARG cc_start: 0.7564 (mmt90) cc_final: 0.7197 (mmt90) REVERT: C 69 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: C 73 ASP cc_start: 0.7117 (m-30) cc_final: 0.6866 (m-30) REVERT: C 140 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7682 (mtt90) REVERT: C 142 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7886 (ttp-110) REVERT: C 172 TRP cc_start: 0.8403 (m100) cc_final: 0.7973 (m100) REVERT: C 177 ASP cc_start: 0.7421 (t0) cc_final: 0.7129 (t0) REVERT: C 186 GLU cc_start: 0.8115 (tp30) cc_final: 0.7794 (tp30) REVERT: C 203 HIS cc_start: 0.7946 (t70) cc_final: 0.7642 (t70) REVERT: C 208 ARG cc_start: 0.8342 (mpp80) cc_final: 0.7939 (mpp80) REVERT: C 220 LEU cc_start: 0.8781 (tt) cc_final: 0.8471 (tt) REVERT: C 242 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 279 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7537 (mtt180) REVERT: C 300 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7507 (tpp-160) REVERT: C 309 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6903 (mp0) REVERT: C 325 ARG cc_start: 0.6706 (tmm-80) cc_final: 0.6371 (ttp80) REVERT: C 342 MET cc_start: 0.4860 (OUTLIER) cc_final: 0.4175 (mmm) REVERT: C 348 PHE cc_start: 0.7151 (t80) cc_final: 0.6739 (t80) REVERT: C 433 ARG cc_start: 0.7382 (tpp-160) cc_final: 0.6574 (mmt-90) REVERT: C 459 ASN cc_start: 0.8516 (m-40) cc_final: 0.8214 (m110) REVERT: C 461 ARG cc_start: 0.7016 (mtm110) cc_final: 0.6747 (mtp180) REVERT: D 22 GLN cc_start: 0.8228 (mt0) cc_final: 0.8004 (mt0) REVERT: D 27 GLN cc_start: 0.8177 (mt0) cc_final: 0.7938 (mm110) REVERT: D 28 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7350 (tm-30) REVERT: D 32 GLN cc_start: 0.8004 (tp40) cc_final: 0.7732 (tp40) REVERT: D 54 ASP cc_start: 0.7735 (t0) cc_final: 0.7179 (t70) REVERT: D 78 TYR cc_start: 0.8547 (t80) cc_final: 0.8244 (t80) REVERT: D 109 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7436 (mt-10) REVERT: D 113 ASP cc_start: 0.7642 (p0) cc_final: 0.7406 (p0) REVERT: D 138 LYS cc_start: 0.8671 (mttt) cc_final: 0.8450 (mttp) REVERT: D 154 TYR cc_start: 0.8556 (t80) cc_final: 0.8216 (t80) REVERT: D 182 GLU cc_start: 0.7338 (tt0) cc_final: 0.6713 (tm-30) REVERT: D 186 GLU cc_start: 0.8000 (tt0) cc_final: 0.7747 (tt0) REVERT: D 204 ASP cc_start: 0.8052 (t70) cc_final: 0.7707 (t0) REVERT: D 211 LEU cc_start: 0.8435 (mp) cc_final: 0.8101 (mt) REVERT: D 219 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7293 (tt0) REVERT: D 226 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8120 (mm-40) REVERT: D 247 TYR cc_start: 0.8481 (m-10) cc_final: 0.8246 (m-10) REVERT: D 329 MET cc_start: 0.7949 (tpp) cc_final: 0.7592 (tpp) REVERT: D 351 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: D 464 PHE cc_start: 0.6497 (p90) cc_final: 0.6067 (p90) outliers start: 69 outliers final: 40 residues processed: 447 average time/residue: 0.1596 time to fit residues: 102.7449 Evaluate side-chains 445 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 397 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 199 HIS B 446 GLN C 92 GLN C 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.188720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140178 restraints weight = 34632.361| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.43 r_work: 0.3350 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20314 Z= 0.150 Angle : 0.537 7.884 28386 Z= 0.295 Chirality : 0.037 0.184 3109 Planarity : 0.004 0.041 3022 Dihedral : 22.590 88.118 4288 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.18 % Allowed : 17.51 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1937 helix: 2.59 (0.17), residues: 914 sheet: 0.16 (0.29), residues: 296 loop : 0.83 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 272 TYR 0.016 0.001 TYR D 188 PHE 0.033 0.001 PHE C 314 TRP 0.020 0.001 TRP A 64 HIS 0.011 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00325 (20298) covalent geometry : angle 0.53063 (28362) hydrogen bonds : bond 0.03555 ( 1060) hydrogen bonds : angle 3.49824 ( 2790) metal coordination : bond 0.00333 ( 16) metal coordination : angle 2.97017 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 405 time to evaluate : 0.628 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: A 27 GLN cc_start: 0.7868 (mt0) cc_final: 0.7513 (mt0) REVERT: A 28 GLN cc_start: 0.8417 (tt0) cc_final: 0.8151 (tt0) REVERT: A 82 ARG cc_start: 0.7987 (mmt180) cc_final: 0.7162 (mmp80) REVERT: A 87 ILE cc_start: 0.8124 (mm) cc_final: 0.7805 (tp) REVERT: A 98 GLU cc_start: 0.7343 (tp30) cc_final: 0.6852 (tp30) REVERT: A 100 HIS cc_start: 0.8016 (m170) cc_final: 0.7673 (m170) REVERT: A 137 ILE cc_start: 0.8545 (mt) cc_final: 0.8290 (tt) REVERT: A 155 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7306 (ptt90) REVERT: A 200 LEU cc_start: 0.8177 (mt) cc_final: 0.7707 (mm) REVERT: A 203 HIS cc_start: 0.7712 (t-90) cc_final: 0.7219 (t-90) REVERT: A 220 LEU cc_start: 0.8347 (mt) cc_final: 0.8041 (tt) REVERT: A 271 THR cc_start: 0.7973 (p) cc_final: 0.7748 (p) REVERT: A 376 GLU cc_start: 0.8440 (tt0) cc_final: 0.8171 (tt0) REVERT: A 383 GLU cc_start: 0.8859 (tt0) cc_final: 0.8473 (tt0) REVERT: A 407 ASP cc_start: 0.8189 (m-30) cc_final: 0.7907 (m-30) REVERT: A 409 ARG cc_start: 0.8652 (ttp-170) cc_final: 0.8352 (ptm160) REVERT: A 455 LEU cc_start: 0.8974 (mt) cc_final: 0.8354 (mm) REVERT: A 458 MET cc_start: 0.7929 (mmm) cc_final: 0.7571 (tmm) REVERT: A 481 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: B 74 VAL cc_start: 0.7815 (t) cc_final: 0.7481 (p) REVERT: B 79 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7356 (mtm180) REVERT: B 135 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 141 ASN cc_start: 0.8541 (m-40) cc_final: 0.8298 (m-40) REVERT: B 143 SER cc_start: 0.8642 (t) cc_final: 0.8334 (m) REVERT: B 155 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8032 (ptt90) REVERT: B 204 ASP cc_start: 0.7893 (t70) cc_final: 0.7688 (t0) REVERT: B 284 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8121 (mtmm) REVERT: B 342 MET cc_start: 0.4861 (ttp) cc_final: 0.4443 (ttp) REVERT: B 371 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 443 TRP cc_start: 0.7717 (t-100) cc_final: 0.7213 (t-100) REVERT: B 456 ARG cc_start: 0.8601 (mtp180) cc_final: 0.8303 (mmm-85) REVERT: B 458 MET cc_start: 0.8234 (mmt) cc_final: 0.7719 (mmp) REVERT: C 10 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.6942 (m) REVERT: C 21 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7445 (tpp80) REVERT: C 24 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 46 VAL cc_start: 0.8621 (t) cc_final: 0.8410 (p) REVERT: C 54 ASP cc_start: 0.8151 (t0) cc_final: 0.7810 (t0) REVERT: C 56 LYS cc_start: 0.7872 (tppp) cc_final: 0.7656 (tppp) REVERT: C 57 ARG cc_start: 0.7523 (mmt90) cc_final: 0.7196 (mmt90) REVERT: C 69 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: C 135 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7826 (mm-30) REVERT: C 172 TRP cc_start: 0.8312 (m100) cc_final: 0.7880 (m100) REVERT: C 177 ASP cc_start: 0.7341 (t0) cc_final: 0.7026 (t0) REVERT: C 186 GLU cc_start: 0.8058 (tp30) cc_final: 0.7632 (tm-30) REVERT: C 203 HIS cc_start: 0.7832 (t70) cc_final: 0.7618 (t70) REVERT: C 208 ARG cc_start: 0.8270 (mpp80) cc_final: 0.7763 (mpp80) REVERT: C 242 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 279 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7497 (mtt180) REVERT: C 300 ARG cc_start: 0.8108 (mmt180) cc_final: 0.7738 (tpp-160) REVERT: C 309 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6868 (mp0) REVERT: C 325 ARG cc_start: 0.6576 (tmm-80) cc_final: 0.6347 (ttp80) REVERT: C 342 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4185 (mmm) REVERT: C 348 PHE cc_start: 0.7101 (t80) cc_final: 0.6812 (t80) REVERT: C 433 ARG cc_start: 0.7244 (tpp-160) cc_final: 0.6446 (mmt-90) REVERT: C 459 ASN cc_start: 0.8451 (m-40) cc_final: 0.8182 (m110) REVERT: C 461 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6717 (mtp180) REVERT: D 27 GLN cc_start: 0.8124 (mt0) cc_final: 0.7807 (mm110) REVERT: D 28 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7359 (tm-30) REVERT: D 32 GLN cc_start: 0.7915 (tp40) cc_final: 0.7672 (tp40) REVERT: D 54 ASP cc_start: 0.7312 (t0) cc_final: 0.7034 (t0) REVERT: D 78 TYR cc_start: 0.8552 (t80) cc_final: 0.8266 (t80) REVERT: D 109 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7411 (mt-10) REVERT: D 154 TYR cc_start: 0.8489 (t80) cc_final: 0.8054 (t80) REVERT: D 182 GLU cc_start: 0.7077 (tt0) cc_final: 0.6520 (tm-30) REVERT: D 186 GLU cc_start: 0.7905 (tt0) cc_final: 0.7671 (tt0) REVERT: D 200 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8504 (mm) REVERT: D 201 VAL cc_start: 0.8534 (t) cc_final: 0.8281 (p) REVERT: D 204 ASP cc_start: 0.7974 (t70) cc_final: 0.7552 (t0) REVERT: D 211 LEU cc_start: 0.8388 (mp) cc_final: 0.8051 (mt) REVERT: D 219 GLN cc_start: 0.7535 (tp-100) cc_final: 0.7245 (tt0) REVERT: D 226 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8060 (mm-40) REVERT: D 247 TYR cc_start: 0.8431 (m-10) cc_final: 0.8217 (m-10) REVERT: D 329 MET cc_start: 0.7744 (tpp) cc_final: 0.7412 (tpp) REVERT: D 351 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: D 409 ARG cc_start: 0.8793 (mmt90) cc_final: 0.8529 (mmt90) REVERT: D 458 MET cc_start: 0.8129 (mmm) cc_final: 0.7781 (mmm) outliers start: 51 outliers final: 31 residues processed: 429 average time/residue: 0.1595 time to fit residues: 98.1459 Evaluate side-chains 443 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 402 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 383 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 486 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 91 GLN B 199 HIS C 251 ASN D 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.184875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135079 restraints weight = 37202.839| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.54 r_work: 0.3275 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 20314 Z= 0.338 Angle : 0.641 9.292 28386 Z= 0.353 Chirality : 0.044 0.202 3109 Planarity : 0.005 0.046 3022 Dihedral : 22.726 86.141 4288 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.24 % Rotamer: Outliers : 3.80 % Allowed : 18.07 % Favored : 78.13 % 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: 1.86 (0.19), residues: 1937 helix: 2.25 (0.17), residues: 913 sheet: -0.02 (0.29), residues: 298 loop : 0.60 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 223 TYR 0.021 0.002 TYR D 324 PHE 0.026 0.002 PHE C 314 TRP 0.025 0.002 TRP B 345 HIS 0.011 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00749 (20298) covalent geometry : angle 0.63320 (28362) hydrogen bonds : bond 0.04642 ( 1060) hydrogen bonds : angle 3.72777 ( 2790) metal coordination : bond 0.00931 ( 16) metal coordination : angle 3.41899 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 422 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7945 (mt0) cc_final: 0.7602 (mt0) REVERT: A 28 GLN cc_start: 0.8475 (tt0) cc_final: 0.8216 (tt0) REVERT: A 69 GLU cc_start: 0.6563 (mp0) cc_final: 0.5887 (mp0) REVERT: A 82 ARG cc_start: 0.7981 (mmt180) cc_final: 0.7315 (mmp80) REVERT: A 87 ILE cc_start: 0.8128 (mm) cc_final: 0.7830 (tp) REVERT: A 98 GLU cc_start: 0.7438 (tp30) cc_final: 0.6905 (tp30) REVERT: A 100 HIS cc_start: 0.7974 (m170) cc_final: 0.7641 (m170) REVERT: A 137 ILE cc_start: 0.8536 (mt) cc_final: 0.8300 (tt) REVERT: A 155 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7103 (ptm160) REVERT: A 164 LEU cc_start: 0.8329 (mm) cc_final: 0.8128 (mt) REVERT: A 182 GLU cc_start: 0.7389 (tt0) cc_final: 0.7105 (tt0) REVERT: A 203 HIS cc_start: 0.7789 (t-90) cc_final: 0.7299 (t-90) REVERT: A 219 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7321 (mm-40) REVERT: A 220 LEU cc_start: 0.8414 (mt) cc_final: 0.8207 (tp) REVERT: A 271 THR cc_start: 0.8058 (p) cc_final: 0.7846 (p) REVERT: A 281 GLU cc_start: 0.8306 (tp30) cc_final: 0.8103 (tp30) REVERT: A 376 GLU cc_start: 0.8445 (tt0) cc_final: 0.8186 (tt0) REVERT: A 383 GLU cc_start: 0.8838 (tt0) cc_final: 0.8470 (tt0) REVERT: A 409 ARG cc_start: 0.8713 (ttp-170) cc_final: 0.8433 (ptm160) REVERT: A 410 ILE cc_start: 0.8677 (mt) cc_final: 0.8449 (mt) REVERT: A 456 ARG cc_start: 0.8654 (mtp180) cc_final: 0.7830 (mtp180) REVERT: A 481 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: B 85 ARG cc_start: 0.8297 (mtt90) cc_final: 0.8072 (mtt90) REVERT: B 109 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7051 (mt-10) REVERT: B 133 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 135 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7828 (mm-30) REVERT: B 141 ASN cc_start: 0.8535 (m-40) cc_final: 0.8167 (m-40) REVERT: B 143 SER cc_start: 0.8666 (t) cc_final: 0.8330 (m) REVERT: B 155 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8151 (ptt180) REVERT: B 204 ASP cc_start: 0.7948 (t70) cc_final: 0.7739 (t0) REVERT: B 284 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8034 (mtmm) REVERT: B 342 MET cc_start: 0.5285 (ttp) cc_final: 0.4789 (ttp) REVERT: B 443 TRP cc_start: 0.7737 (t-100) cc_final: 0.7274 (t-100) REVERT: B 456 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8216 (mmm-85) REVERT: B 458 MET cc_start: 0.8270 (mmt) cc_final: 0.7674 (mmp) REVERT: C 21 ARG cc_start: 0.7797 (mmm160) cc_final: 0.7517 (tpp80) REVERT: C 24 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 46 VAL cc_start: 0.8681 (t) cc_final: 0.8430 (p) REVERT: C 54 ASP cc_start: 0.8169 (t0) cc_final: 0.7875 (t0) REVERT: C 69 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: C 70 GLN cc_start: 0.8685 (mp10) cc_final: 0.8480 (mp10) REVERT: C 142 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7838 (ttp-110) REVERT: C 172 TRP cc_start: 0.8393 (m100) cc_final: 0.7942 (m100) REVERT: C 177 ASP cc_start: 0.7399 (t0) cc_final: 0.7162 (t0) REVERT: C 186 GLU cc_start: 0.8092 (tp30) cc_final: 0.7779 (tp30) REVERT: C 203 HIS cc_start: 0.7855 (t70) cc_final: 0.7568 (t70) REVERT: C 208 ARG cc_start: 0.8268 (mpp80) cc_final: 0.7936 (mpp80) REVERT: C 220 LEU cc_start: 0.8774 (tt) cc_final: 0.8480 (tt) REVERT: C 240 ILE cc_start: 0.8222 (mm) cc_final: 0.7924 (tt) REVERT: C 242 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7652 (mt-10) REVERT: C 279 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7553 (mtt180) REVERT: C 300 ARG cc_start: 0.8139 (mmt180) cc_final: 0.7800 (tpp-160) REVERT: C 303 PHE cc_start: 0.7336 (m-80) cc_final: 0.7036 (m-80) REVERT: C 309 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7098 (mp0) REVERT: C 313 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7143 (tttp) REVERT: C 342 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.4389 (mmm) REVERT: C 348 PHE cc_start: 0.7191 (t80) cc_final: 0.6786 (t80) REVERT: C 459 ASN cc_start: 0.8637 (m-40) cc_final: 0.8403 (m110) REVERT: C 461 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6735 (mtp180) REVERT: D 20 GLU cc_start: 0.7627 (mp0) cc_final: 0.7142 (mp0) REVERT: D 22 GLN cc_start: 0.8220 (mt0) cc_final: 0.8014 (mt0) REVERT: D 27 GLN cc_start: 0.8163 (mt0) cc_final: 0.7942 (mm110) REVERT: D 28 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7344 (tm-30) REVERT: D 32 GLN cc_start: 0.7979 (tp40) cc_final: 0.7687 (tp40) REVERT: D 54 ASP cc_start: 0.7634 (t0) cc_final: 0.7278 (t0) REVERT: D 68 GLU cc_start: 0.8239 (tt0) cc_final: 0.7781 (tt0) REVERT: D 78 TYR cc_start: 0.8547 (t80) cc_final: 0.8310 (t80) REVERT: D 109 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 113 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7437 (p0) REVERT: D 118 PHE cc_start: 0.8377 (m-10) cc_final: 0.8138 (m-10) REVERT: D 154 TYR cc_start: 0.8550 (t80) cc_final: 0.8230 (t80) REVERT: D 182 GLU cc_start: 0.7226 (tt0) cc_final: 0.6654 (tm-30) REVERT: D 186 GLU cc_start: 0.7937 (tt0) cc_final: 0.7690 (tt0) REVERT: D 211 LEU cc_start: 0.8401 (mp) cc_final: 0.8101 (mt) REVERT: D 219 GLN cc_start: 0.7652 (tp-100) cc_final: 0.7298 (tt0) REVERT: D 226 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8089 (mm-40) REVERT: D 229 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7257 (pp20) REVERT: D 247 TYR cc_start: 0.8455 (m-10) cc_final: 0.8207 (m-10) REVERT: D 329 MET cc_start: 0.7975 (tpp) cc_final: 0.7599 (tpp) REVERT: D 409 ARG cc_start: 0.8812 (mmt90) cc_final: 0.8503 (mmt90) REVERT: D 464 PHE cc_start: 0.6409 (p90) cc_final: 0.6118 (p90) outliers start: 61 outliers final: 42 residues processed: 455 average time/residue: 0.1638 time to fit residues: 106.7052 Evaluate side-chains 462 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 411 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 138 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 274 GLN B 91 GLN B 199 HIS C 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.188341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142636 restraints weight = 31953.315| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.36 r_work: 0.3338 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20314 Z= 0.153 Angle : 0.555 8.158 28386 Z= 0.304 Chirality : 0.037 0.159 3109 Planarity : 0.004 0.041 3022 Dihedral : 22.610 88.546 4288 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.29 % Favored : 98.66 % Rotamer: Outliers : 3.12 % Allowed : 19.56 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 1937 helix: 2.52 (0.17), residues: 912 sheet: -0.03 (0.28), residues: 320 loop : 0.79 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 433 TYR 0.017 0.002 TYR D 188 PHE 0.040 0.001 PHE C 314 TRP 0.037 0.001 TRP B 345 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00331 (20298) covalent geometry : angle 0.54840 (28362) hydrogen bonds : bond 0.03594 ( 1060) hydrogen bonds : angle 3.54963 ( 2790) metal coordination : bond 0.00327 ( 16) metal coordination : angle 2.96922 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 420 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7944 (mt0) cc_final: 0.7610 (mt0) REVERT: A 28 GLN cc_start: 0.8447 (tt0) cc_final: 0.8160 (tt0) REVERT: A 69 GLU cc_start: 0.6326 (mp0) cc_final: 0.5591 (mt-10) REVERT: A 87 ILE cc_start: 0.8161 (mm) cc_final: 0.7847 (tp) REVERT: A 98 GLU cc_start: 0.7395 (tp30) cc_final: 0.6796 (tp30) REVERT: A 100 HIS cc_start: 0.8027 (m170) cc_final: 0.7639 (m170) REVERT: A 137 ILE cc_start: 0.8568 (mt) cc_final: 0.8326 (tt) REVERT: A 155 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7429 (ptt90) REVERT: A 203 HIS cc_start: 0.7757 (t-90) cc_final: 0.7229 (t-90) REVERT: A 219 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7223 (mm-40) REVERT: A 220 LEU cc_start: 0.8375 (mt) cc_final: 0.8091 (tt) REVERT: A 376 GLU cc_start: 0.8437 (tt0) cc_final: 0.8179 (tt0) REVERT: A 383 GLU cc_start: 0.8797 (tt0) cc_final: 0.8420 (tt0) REVERT: A 407 ASP cc_start: 0.8061 (m-30) cc_final: 0.7748 (p0) REVERT: A 409 ARG cc_start: 0.8629 (ttp-170) cc_final: 0.8295 (ptm160) REVERT: A 456 ARG cc_start: 0.8588 (mtp180) cc_final: 0.7710 (mtp180) REVERT: A 481 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: B 74 VAL cc_start: 0.7935 (t) cc_final: 0.7584 (p) REVERT: B 79 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7275 (mtm180) REVERT: B 102 LYS cc_start: 0.8294 (mptt) cc_final: 0.7921 (mptt) REVERT: B 116 THR cc_start: 0.8488 (t) cc_final: 0.8170 (p) REVERT: B 135 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 141 ASN cc_start: 0.8559 (m-40) cc_final: 0.8323 (m-40) REVERT: B 143 SER cc_start: 0.8679 (t) cc_final: 0.8372 (m) REVERT: B 155 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8107 (ptt90) REVERT: B 204 ASP cc_start: 0.7895 (t70) cc_final: 0.7678 (t0) REVERT: B 284 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8027 (mtmm) REVERT: B 342 MET cc_start: 0.5253 (ttp) cc_final: 0.4796 (ttp) REVERT: B 443 TRP cc_start: 0.7700 (t-100) cc_final: 0.7248 (t-100) REVERT: B 456 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8287 (mmm-85) REVERT: B 458 MET cc_start: 0.8246 (mmt) cc_final: 0.7701 (mmt) REVERT: C 10 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7117 (m) REVERT: C 46 VAL cc_start: 0.8649 (t) cc_final: 0.8437 (p) REVERT: C 54 ASP cc_start: 0.8182 (t0) cc_final: 0.7864 (t0) REVERT: C 69 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: C 142 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7857 (ttp-110) REVERT: C 172 TRP cc_start: 0.8361 (m100) cc_final: 0.7893 (m100) REVERT: C 177 ASP cc_start: 0.7348 (t0) cc_final: 0.7019 (t0) REVERT: C 186 GLU cc_start: 0.8077 (tp30) cc_final: 0.7756 (tp30) REVERT: C 203 HIS cc_start: 0.7874 (t70) cc_final: 0.7602 (t70) REVERT: C 208 ARG cc_start: 0.8263 (mpp80) cc_final: 0.7977 (mpp80) REVERT: C 220 LEU cc_start: 0.8765 (tt) cc_final: 0.8479 (tt) REVERT: C 242 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 279 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7468 (mtt180) REVERT: C 300 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7742 (tpp-160) REVERT: C 309 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7101 (mp0) REVERT: C 313 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7227 (tttp) REVERT: C 342 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.4318 (mmm) REVERT: C 348 PHE cc_start: 0.7147 (t80) cc_final: 0.6780 (t80) REVERT: C 459 ASN cc_start: 0.8562 (m-40) cc_final: 0.8318 (m110) REVERT: C 461 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6765 (mtp180) REVERT: D 20 GLU cc_start: 0.7626 (mp0) cc_final: 0.7168 (mp0) REVERT: D 27 GLN cc_start: 0.8147 (mt0) cc_final: 0.7860 (mm110) REVERT: D 28 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7425 (tm-30) REVERT: D 68 GLU cc_start: 0.8162 (tt0) cc_final: 0.7618 (tt0) REVERT: D 78 TYR cc_start: 0.8551 (t80) cc_final: 0.8336 (t80) REVERT: D 109 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7396 (mt-10) REVERT: D 118 PHE cc_start: 0.8359 (m-10) cc_final: 0.8054 (m-10) REVERT: D 154 TYR cc_start: 0.8510 (t80) cc_final: 0.8135 (t80) REVERT: D 182 GLU cc_start: 0.7034 (tt0) cc_final: 0.6424 (tm-30) REVERT: D 186 GLU cc_start: 0.7877 (tt0) cc_final: 0.7643 (tt0) REVERT: D 211 LEU cc_start: 0.8383 (mp) cc_final: 0.8105 (mt) REVERT: D 219 GLN cc_start: 0.7514 (tp-100) cc_final: 0.7236 (tt0) REVERT: D 229 GLU cc_start: 0.7540 (pp20) cc_final: 0.7272 (pp20) REVERT: D 247 TYR cc_start: 0.8421 (m-10) cc_final: 0.8185 (m-10) REVERT: D 329 MET cc_start: 0.7799 (tpp) cc_final: 0.7464 (tpp) REVERT: D 348 PHE cc_start: 0.7469 (t80) cc_final: 0.7078 (t80) REVERT: D 351 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7233 (pt0) REVERT: D 409 ARG cc_start: 0.8780 (mmt90) cc_final: 0.8569 (mmt90) REVERT: D 458 MET cc_start: 0.8135 (mmm) cc_final: 0.7734 (mmm) REVERT: D 464 PHE cc_start: 0.6344 (p90) cc_final: 0.6060 (p90) outliers start: 50 outliers final: 36 residues processed: 449 average time/residue: 0.1606 time to fit residues: 103.7195 Evaluate side-chains 458 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 413 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 383 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 486 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 199 HIS C 251 ASN D 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.188032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137542 restraints weight = 52084.904| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.11 r_work: 0.3288 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20314 Z= 0.170 Angle : 0.565 10.741 28386 Z= 0.309 Chirality : 0.038 0.163 3109 Planarity : 0.004 0.040 3022 Dihedral : 22.579 87.280 4285 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.55 % Favored : 98.40 % Rotamer: Outliers : 3.24 % Allowed : 19.50 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 1937 helix: 2.52 (0.17), residues: 913 sheet: -0.02 (0.29), residues: 310 loop : 0.82 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 433 TYR 0.017 0.002 TYR D 188 PHE 0.020 0.001 PHE C 314 TRP 0.036 0.001 TRP B 345 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00372 (20298) covalent geometry : angle 0.55909 (28362) hydrogen bonds : bond 0.03663 ( 1060) hydrogen bonds : angle 3.54165 ( 2790) metal coordination : bond 0.00411 ( 16) metal coordination : angle 2.83564 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 411 time to evaluate : 0.475 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: A 27 GLN cc_start: 0.7962 (mt0) cc_final: 0.7631 (mt0) REVERT: A 28 GLN cc_start: 0.8492 (tt0) cc_final: 0.8191 (tt0) REVERT: A 69 GLU cc_start: 0.6305 (mp0) cc_final: 0.5577 (mt-10) REVERT: A 86 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 87 ILE cc_start: 0.8153 (mm) cc_final: 0.7866 (tp) REVERT: A 98 GLU cc_start: 0.7429 (tp30) cc_final: 0.6829 (tp30) REVERT: A 100 HIS cc_start: 0.8035 (m170) cc_final: 0.7637 (m170) REVERT: A 137 ILE cc_start: 0.8562 (mt) cc_final: 0.8323 (tt) REVERT: A 155 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7459 (ptt90) REVERT: A 182 GLU cc_start: 0.7180 (tt0) cc_final: 0.6924 (tt0) REVERT: A 203 HIS cc_start: 0.7769 (t-90) cc_final: 0.7217 (t-90) REVERT: A 219 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7343 (mm-40) REVERT: A 220 LEU cc_start: 0.8378 (mt) cc_final: 0.8134 (tp) REVERT: A 223 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7756 (mtm-85) REVERT: A 376 GLU cc_start: 0.8443 (tt0) cc_final: 0.8185 (tt0) REVERT: A 383 GLU cc_start: 0.8847 (tt0) cc_final: 0.8477 (tt0) REVERT: A 409 ARG cc_start: 0.8678 (ttp-170) cc_final: 0.8315 (ptm160) REVERT: A 456 ARG cc_start: 0.8574 (mtp180) cc_final: 0.7732 (mtp180) REVERT: A 481 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: B 74 VAL cc_start: 0.7916 (t) cc_final: 0.7559 (p) REVERT: B 133 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 135 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 141 ASN cc_start: 0.8569 (m-40) cc_final: 0.8292 (m-40) REVERT: B 143 SER cc_start: 0.8663 (t) cc_final: 0.8353 (m) REVERT: B 155 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8002 (ppt170) REVERT: B 204 ASP cc_start: 0.7936 (t70) cc_final: 0.7715 (t0) REVERT: B 284 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8097 (mtmm) REVERT: B 342 MET cc_start: 0.5170 (ttp) cc_final: 0.4724 (ttp) REVERT: B 443 TRP cc_start: 0.7780 (t-100) cc_final: 0.7292 (t-100) REVERT: B 447 ASP cc_start: 0.8157 (p0) cc_final: 0.7673 (t0) REVERT: B 456 ARG cc_start: 0.8604 (mtp180) cc_final: 0.8287 (mmm-85) REVERT: B 458 MET cc_start: 0.8288 (mmt) cc_final: 0.7730 (mmt) REVERT: C 10 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7294 (m) REVERT: C 24 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7675 (tm-30) REVERT: C 27 GLN cc_start: 0.8062 (mt0) cc_final: 0.7795 (mt0) REVERT: C 46 VAL cc_start: 0.8674 (t) cc_final: 0.8445 (p) REVERT: C 54 ASP cc_start: 0.8178 (t0) cc_final: 0.7837 (t0) REVERT: C 69 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: C 142 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7896 (ttp-110) REVERT: C 172 TRP cc_start: 0.8402 (m100) cc_final: 0.7864 (m100) REVERT: C 177 ASP cc_start: 0.7480 (t0) cc_final: 0.7128 (t0) REVERT: C 186 GLU cc_start: 0.8078 (tp30) cc_final: 0.7747 (tp30) REVERT: C 203 HIS cc_start: 0.7931 (t70) cc_final: 0.7641 (t70) REVERT: C 208 ARG cc_start: 0.8310 (mpp80) cc_final: 0.7964 (mpp80) REVERT: C 242 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 279 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7551 (mtt180) REVERT: C 300 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7744 (tpp-160) REVERT: C 303 PHE cc_start: 0.7344 (m-80) cc_final: 0.7116 (m-80) REVERT: C 309 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7160 (mp0) REVERT: C 313 LYS cc_start: 0.7792 (ttpp) cc_final: 0.6993 (ttpp) REVERT: C 342 MET cc_start: 0.4897 (OUTLIER) cc_final: 0.4441 (mmm) REVERT: C 348 PHE cc_start: 0.7138 (t80) cc_final: 0.6785 (t80) REVERT: C 459 ASN cc_start: 0.8558 (m-40) cc_final: 0.8319 (m110) REVERT: C 461 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6752 (mtp180) REVERT: D 20 GLU cc_start: 0.7682 (mp0) cc_final: 0.7181 (mp0) REVERT: D 22 GLN cc_start: 0.8198 (mt0) cc_final: 0.7982 (mt0) REVERT: D 54 ASP cc_start: 0.7425 (t0) cc_final: 0.7098 (t0) REVERT: D 68 GLU cc_start: 0.8248 (tt0) cc_final: 0.7730 (tt0) REVERT: D 78 TYR cc_start: 0.8574 (t80) cc_final: 0.8357 (t80) REVERT: D 109 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 113 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7339 (p0) REVERT: D 118 PHE cc_start: 0.8389 (m-10) cc_final: 0.8094 (m-10) REVERT: D 154 TYR cc_start: 0.8509 (t80) cc_final: 0.8119 (t80) REVERT: D 182 GLU cc_start: 0.7098 (tt0) cc_final: 0.6446 (tm-30) REVERT: D 186 GLU cc_start: 0.7946 (tt0) cc_final: 0.7725 (tt0) REVERT: D 211 LEU cc_start: 0.8419 (mp) cc_final: 0.8129 (mt) REVERT: D 219 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7312 (tt0) REVERT: D 229 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7319 (pp20) REVERT: D 247 TYR cc_start: 0.8466 (m-10) cc_final: 0.8250 (m-10) REVERT: D 329 MET cc_start: 0.7853 (tpp) cc_final: 0.7504 (tpp) REVERT: D 409 ARG cc_start: 0.8844 (mmt90) cc_final: 0.8607 (mmt90) REVERT: D 464 PHE cc_start: 0.6332 (p90) cc_final: 0.6074 (p90) outliers start: 52 outliers final: 37 residues processed: 439 average time/residue: 0.1551 time to fit residues: 97.7276 Evaluate side-chains 456 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 408 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 242 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 9.9990 chunk 16 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 22 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 226 GLN B 91 GLN B 199 HIS B 446 GLN C 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131198 restraints weight = 37151.165| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.58 r_work: 0.3211 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.159 20314 Z= 0.646 Angle : 0.852 11.464 28386 Z= 0.469 Chirality : 0.060 0.298 3109 Planarity : 0.007 0.085 3022 Dihedral : 23.042 89.218 4285 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 3.93 % Allowed : 19.00 % Favored : 77.07 % 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: 0.72 (0.19), residues: 1937 helix: 1.25 (0.16), residues: 919 sheet: -0.63 (0.29), residues: 300 loop : 0.16 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 155 TYR 0.036 0.004 TYR B 163 PHE 0.034 0.003 PHE C 118 TRP 0.053 0.003 TRP B 345 HIS 0.021 0.002 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.01431 (20298) covalent geometry : angle 0.84150 (28362) hydrogen bonds : bond 0.06610 ( 1060) hydrogen bonds : angle 4.24945 ( 2790) metal coordination : bond 0.01891 ( 16) metal coordination : angle 4.74255 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 423 time to evaluate : 0.611 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: A 8 ARG cc_start: 0.6348 (ttp80) cc_final: 0.5641 (ttp80) REVERT: A 22 GLN cc_start: 0.8285 (mt0) cc_final: 0.8044 (mt0) REVERT: A 23 LEU cc_start: 0.8615 (tp) cc_final: 0.8405 (tp) REVERT: A 27 GLN cc_start: 0.8076 (mt0) cc_final: 0.7852 (mt0) REVERT: A 28 GLN cc_start: 0.8574 (tt0) cc_final: 0.8278 (tt0) REVERT: A 89 HIS cc_start: 0.8007 (m170) cc_final: 0.7740 (m90) REVERT: A 98 GLU cc_start: 0.7457 (tp30) cc_final: 0.6929 (tp30) REVERT: A 100 HIS cc_start: 0.8023 (m170) cc_final: 0.7741 (m170) REVERT: A 113 ASP cc_start: 0.7398 (m-30) cc_final: 0.7115 (m-30) REVERT: A 137 ILE cc_start: 0.8465 (mt) cc_final: 0.8265 (tt) REVERT: A 155 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7452 (ptt90) REVERT: A 182 GLU cc_start: 0.7593 (tt0) cc_final: 0.7317 (tt0) REVERT: A 200 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8185 (mt) REVERT: A 203 HIS cc_start: 0.8007 (t-90) cc_final: 0.7522 (t-90) REVERT: A 219 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7314 (mm-40) REVERT: A 271 THR cc_start: 0.8221 (p) cc_final: 0.7988 (p) REVERT: A 376 GLU cc_start: 0.8603 (tt0) cc_final: 0.8359 (tt0) REVERT: A 383 GLU cc_start: 0.8890 (tt0) cc_final: 0.8461 (tt0) REVERT: A 409 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8423 (ptm160) REVERT: A 456 ARG cc_start: 0.8770 (mtp180) cc_final: 0.7876 (mtp180) REVERT: A 481 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: B 133 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 135 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 155 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8310 (ptt90) REVERT: B 204 ASP cc_start: 0.8031 (t70) cc_final: 0.7795 (t0) REVERT: B 284 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8028 (mtmm) REVERT: B 342 MET cc_start: 0.5303 (ttp) cc_final: 0.4845 (ttp) REVERT: B 375 VAL cc_start: 0.8677 (p) cc_final: 0.8407 (m) REVERT: B 443 TRP cc_start: 0.7843 (t-100) cc_final: 0.7342 (t-100) REVERT: B 458 MET cc_start: 0.8399 (mmt) cc_final: 0.7846 (mmt) REVERT: B 459 ASN cc_start: 0.8360 (m-40) cc_final: 0.7985 (m-40) REVERT: C 10 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8036 (m) REVERT: C 24 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7620 (tm-30) REVERT: C 45 ASP cc_start: 0.7886 (t0) cc_final: 0.7499 (t0) REVERT: C 69 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: C 142 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7940 (ttp-110) REVERT: C 172 TRP cc_start: 0.8419 (m100) cc_final: 0.7821 (m100) REVERT: C 177 ASP cc_start: 0.7469 (t0) cc_final: 0.7259 (t0) REVERT: C 186 GLU cc_start: 0.8188 (tp30) cc_final: 0.7697 (tp30) REVERT: C 203 HIS cc_start: 0.7890 (t70) cc_final: 0.7527 (t70) REVERT: C 204 ASP cc_start: 0.8211 (t70) cc_final: 0.7867 (t70) REVERT: C 208 ARG cc_start: 0.8232 (mpp80) cc_final: 0.7865 (mpp80) REVERT: C 220 LEU cc_start: 0.8784 (tt) cc_final: 0.8468 (tt) REVERT: C 242 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7635 (mt-10) REVERT: C 279 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7539 (mtt180) REVERT: C 300 ARG cc_start: 0.8166 (mmt180) cc_final: 0.7696 (tpp-160) REVERT: C 303 PHE cc_start: 0.7547 (m-80) cc_final: 0.7341 (m-80) REVERT: C 309 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7344 (mp0) REVERT: C 342 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4592 (mmm) REVERT: C 459 ASN cc_start: 0.8800 (m-40) cc_final: 0.8579 (m110) REVERT: C 461 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6679 (mtp180) REVERT: D 20 GLU cc_start: 0.7737 (mp0) cc_final: 0.7230 (mp0) REVERT: D 27 GLN cc_start: 0.8214 (mm110) cc_final: 0.8007 (mm-40) REVERT: D 32 GLN cc_start: 0.7942 (tp40) cc_final: 0.7622 (tp40) REVERT: D 68 GLU cc_start: 0.8250 (tt0) cc_final: 0.7810 (tt0) REVERT: D 78 TYR cc_start: 0.8549 (t80) cc_final: 0.8297 (t80) REVERT: D 109 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 113 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7452 (p0) REVERT: D 182 GLU cc_start: 0.7524 (tt0) cc_final: 0.6970 (tm-30) REVERT: D 186 GLU cc_start: 0.7887 (tt0) cc_final: 0.7646 (tt0) REVERT: D 219 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7554 (tt0) REVERT: D 229 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7218 (pp20) REVERT: D 247 TYR cc_start: 0.8462 (m-10) cc_final: 0.8251 (m-10) REVERT: D 342 MET cc_start: 0.5493 (ptt) cc_final: 0.5276 (ptt) REVERT: D 409 ARG cc_start: 0.8942 (mmt90) cc_final: 0.8742 (mmt90) REVERT: D 464 PHE cc_start: 0.6599 (p90) cc_final: 0.6291 (p90) outliers start: 63 outliers final: 47 residues processed: 452 average time/residue: 0.1596 time to fit residues: 104.2263 Evaluate side-chains 474 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 416 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 138 optimal weight: 50.0000 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 199 HIS B 446 GLN C 251 ASN D 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.187715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138468 restraints weight = 37943.390| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.59 r_work: 0.3337 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20314 Z= 0.153 Angle : 0.611 10.698 28386 Z= 0.332 Chirality : 0.038 0.165 3109 Planarity : 0.005 0.046 3022 Dihedral : 22.835 88.989 4284 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.30 % Rotamer: Outliers : 2.62 % Allowed : 20.75 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.20), residues: 1937 helix: 2.18 (0.17), residues: 911 sheet: -0.39 (0.28), residues: 300 loop : 0.54 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 325 TYR 0.017 0.002 TYR C 324 PHE 0.019 0.002 PHE C 118 TRP 0.025 0.001 TRP B 345 HIS 0.013 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00333 (20298) covalent geometry : angle 0.60387 (28362) hydrogen bonds : bond 0.03807 ( 1060) hydrogen bonds : angle 3.71652 ( 2790) metal coordination : bond 0.00393 ( 16) metal coordination : angle 3.35651 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 413 time to evaluate : 0.561 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: A 8 ARG cc_start: 0.6028 (ttp80) cc_final: 0.5143 (ttp80) REVERT: A 22 GLN cc_start: 0.8139 (mt0) cc_final: 0.7860 (mt0) REVERT: A 23 LEU cc_start: 0.8436 (tp) cc_final: 0.8207 (tp) REVERT: A 27 GLN cc_start: 0.7998 (mt0) cc_final: 0.7775 (mt0) REVERT: A 28 GLN cc_start: 0.8467 (tt0) cc_final: 0.8162 (tt0) REVERT: A 69 GLU cc_start: 0.6421 (mp0) cc_final: 0.5786 (mt-10) REVERT: A 82 ARG cc_start: 0.7935 (mmt180) cc_final: 0.7091 (mmt180) REVERT: A 98 GLU cc_start: 0.7350 (tp30) cc_final: 0.6801 (tp30) REVERT: A 100 HIS cc_start: 0.8002 (m170) cc_final: 0.7637 (m170) REVERT: A 137 ILE cc_start: 0.8560 (mt) cc_final: 0.8326 (tt) REVERT: A 155 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7426 (ptt-90) REVERT: A 169 ASP cc_start: 0.7590 (t0) cc_final: 0.7372 (t0) REVERT: A 182 GLU cc_start: 0.7119 (tt0) cc_final: 0.6865 (tt0) REVERT: A 196 GLU cc_start: 0.8310 (pt0) cc_final: 0.7699 (pt0) REVERT: A 203 HIS cc_start: 0.7820 (t-90) cc_final: 0.7303 (t-90) REVERT: A 240 ILE cc_start: 0.8523 (mt) cc_final: 0.8209 (tt) REVERT: A 271 THR cc_start: 0.8054 (p) cc_final: 0.7825 (p) REVERT: A 273 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: A 376 GLU cc_start: 0.8400 (tt0) cc_final: 0.8125 (tt0) REVERT: A 383 GLU cc_start: 0.8773 (tt0) cc_final: 0.8403 (tt0) REVERT: A 409 ARG cc_start: 0.8709 (ttp-170) cc_final: 0.8391 (ptm160) REVERT: A 456 ARG cc_start: 0.8596 (mtp180) cc_final: 0.7769 (mtp180) REVERT: A 481 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: B 27 GLN cc_start: 0.8071 (mt0) cc_final: 0.7832 (mm-40) REVERT: B 73 ASP cc_start: 0.8063 (m-30) cc_final: 0.7696 (m-30) REVERT: B 102 LYS cc_start: 0.8305 (mptt) cc_final: 0.7827 (mmtm) REVERT: B 133 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 135 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 141 ASN cc_start: 0.8521 (m-40) cc_final: 0.8242 (m-40) REVERT: B 193 ASP cc_start: 0.7560 (m-30) cc_final: 0.7358 (m-30) REVERT: B 204 ASP cc_start: 0.7912 (t70) cc_final: 0.7691 (t0) REVERT: B 284 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8117 (mtmm) REVERT: B 342 MET cc_start: 0.5508 (ttp) cc_final: 0.5016 (ttp) REVERT: B 443 TRP cc_start: 0.7607 (t-100) cc_final: 0.7244 (t-100) REVERT: B 447 ASP cc_start: 0.8179 (p0) cc_final: 0.7784 (t70) REVERT: B 456 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8157 (mmm-85) REVERT: B 458 MET cc_start: 0.8234 (mmt) cc_final: 0.7630 (mmt) REVERT: C 24 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 54 ASP cc_start: 0.8090 (t0) cc_final: 0.7719 (t0) REVERT: C 57 ARG cc_start: 0.7549 (mmt90) cc_final: 0.7218 (mmt90) REVERT: C 69 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: C 70 GLN cc_start: 0.8616 (mp10) cc_final: 0.8394 (mp10) REVERT: C 142 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7848 (ttp-110) REVERT: C 172 TRP cc_start: 0.8299 (m100) cc_final: 0.7884 (m100) REVERT: C 186 GLU cc_start: 0.8081 (tp30) cc_final: 0.7661 (tm-30) REVERT: C 203 HIS cc_start: 0.7781 (t70) cc_final: 0.7478 (t70) REVERT: C 208 ARG cc_start: 0.8281 (mpp80) cc_final: 0.7991 (mpp80) REVERT: C 242 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 264 VAL cc_start: 0.8196 (t) cc_final: 0.7994 (m) REVERT: C 279 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7386 (mtt180) REVERT: C 300 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7656 (tpp-160) REVERT: C 303 PHE cc_start: 0.7261 (m-80) cc_final: 0.6902 (m-80) REVERT: C 309 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7302 (mp0) REVERT: C 313 LYS cc_start: 0.7481 (ttpp) cc_final: 0.6919 (ttpp) REVERT: C 342 MET cc_start: 0.5401 (OUTLIER) cc_final: 0.5064 (mmm) REVERT: C 348 PHE cc_start: 0.7314 (t80) cc_final: 0.6772 (t80) REVERT: C 459 ASN cc_start: 0.8600 (m-40) cc_final: 0.8354 (m110) REVERT: D 20 GLU cc_start: 0.7640 (mp0) cc_final: 0.7171 (mp0) REVERT: D 54 ASP cc_start: 0.7503 (t0) cc_final: 0.7177 (t0) REVERT: D 68 GLU cc_start: 0.8172 (tt0) cc_final: 0.7592 (tt0) REVERT: D 78 TYR cc_start: 0.8539 (t80) cc_final: 0.8334 (t80) REVERT: D 109 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7429 (mt-10) REVERT: D 113 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7238 (p0) REVERT: D 154 TYR cc_start: 0.8508 (t80) cc_final: 0.8071 (t80) REVERT: D 182 GLU cc_start: 0.7154 (tt0) cc_final: 0.6578 (tm-30) REVERT: D 186 GLU cc_start: 0.7870 (tt0) cc_final: 0.7610 (tt0) REVERT: D 211 LEU cc_start: 0.8320 (mp) cc_final: 0.8003 (mt) REVERT: D 219 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7186 (tt0) REVERT: D 229 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: D 247 TYR cc_start: 0.8457 (m-10) cc_final: 0.8252 (m-10) REVERT: D 329 MET cc_start: 0.7937 (tpp) cc_final: 0.7582 (tpp) REVERT: D 464 PHE cc_start: 0.6363 (p90) cc_final: 0.6068 (p90) outliers start: 42 outliers final: 29 residues processed: 434 average time/residue: 0.1613 time to fit residues: 100.2302 Evaluate side-chains 447 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 410 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 229 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 106 optimal weight: 0.0570 chunk 98 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 7 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 47 optimal weight: 7.9990 chunk 90 optimal weight: 0.0770 chunk 33 optimal weight: 50.0000 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 195 HIS A 219 GLN B 199 HIS C 251 ASN C 352 GLN D 27 GLN D 203 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.189635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141594 restraints weight = 35432.450| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.51 r_work: 0.3382 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20314 Z= 0.133 Angle : 0.581 11.830 28386 Z= 0.315 Chirality : 0.037 0.163 3109 Planarity : 0.005 0.058 3022 Dihedral : 22.735 87.899 4280 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.37 % Allowed : 20.93 % Favored : 76.70 % 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: 1.91 (0.20), residues: 1937 helix: 2.39 (0.17), residues: 911 sheet: -0.32 (0.29), residues: 309 loop : 0.66 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 325 TYR 0.018 0.001 TYR D 188 PHE 0.015 0.001 PHE A 348 TRP 0.019 0.001 TRP D 96 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00283 (20298) covalent geometry : angle 0.57600 (28362) hydrogen bonds : bond 0.03450 ( 1060) hydrogen bonds : angle 3.63976 ( 2790) metal coordination : bond 0.00274 ( 16) metal coordination : angle 2.69614 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6343.21 seconds wall clock time: 108 minutes 24.46 seconds (6504.46 seconds total)