Starting phenix.real_space_refine on Sat Jul 4 09:57:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu2_60887/07_2026/9iu2_60887.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu2_60887/07_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_60887/07_2026/9iu2_60887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu2_60887/07_2026/9iu2_60887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu2_60887/07_2026/9iu2_60887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu2_60887/07_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-dev-6108/lib/python3.11/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: 4.55, per 1000 atoms: 0.23 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: 1.18 Conformation dependent library (CDL) restraints added in 796.6 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: 2.27 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: 3.31 Time building geometry restraints manager: 1.73 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=" N1 DC E 30 " pdb=" C6 DC E 30 " ideal model delta sigma weight residual 1.367 1.314 0.053 6.00e-03 2.78e+04 7.90e+01 bond pdb=" N1 DC F 21 " pdb=" C6 DC F 21 " ideal model delta sigma weight residual 1.367 1.321 0.046 6.00e-03 2.78e+04 5.90e+01 bond pdb=" N1 DCG2 27 " pdb=" C6 DCG2 27 " ideal model delta sigma weight residual 1.367 1.326 0.041 6.00e-03 2.78e+04 4.75e+01 bond pdb=" C4 DC F 30 " pdb=" C5 DC F 30 " ideal model delta sigma weight residual 1.425 1.375 0.050 8.00e-03 1.56e+04 3.86e+01 bond pdb=" N1 DCH2 18 " pdb=" C6 DCH2 18 " ideal model delta sigma weight residual 1.367 1.330 0.037 6.00e-03 2.78e+04 3.75e+01 ... (remaining 20293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 27060 4.30 - 8.59: 1241 8.59 - 12.89: 54 12.89 - 17.19: 5 17.19 - 21.48: 2 Bond angle restraints: 28362 Sorted by residual: angle pdb=" O4' DTH2 23 " pdb=" C4' DTH2 23 " pdb=" C3' DTH2 23 " ideal model delta sigma weight residual 106.00 97.18 8.82 6.00e-01 2.78e+00 2.16e+02 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=" O4' DCG1 18 " pdb=" C1' DCG1 18 " pdb=" N1 DCG1 18 " ideal model delta sigma weight residual 108.00 115.54 -7.54 7.00e-01 2.04e+00 1.16e+02 ... (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 - 0.130: 2599 0.130 - 0.260: 452 0.260 - 0.390: 45 0.390 - 0.520: 9 0.520 - 0.651: 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 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+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 2.34 2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 ... (remaining 3106 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" 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: 0.890 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.740 Find NCS groups from input model: 0.380 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 : 0.012 0.242 20314 Z= 0.778 Angle : 1.999 21.484 28386 Z= 1.351 Chirality : 0.100 0.651 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/Z covalent geometry : bond 0.01112 / 0.77 (20298) covalent geometry : angle 1.97873 / 1.35 (28362) hydrogen bonds : bond 0.14866 / 10.05 ( 1060) hydrogen bonds : angle 5.75735 / 4.17 ( 2790) metal coordination : bond 0.12751 / 7.28 ( 16) metal coordination : angle 9.93878 / 6.49 ( 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 : 0.621 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: 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: 0.1789 time to fit residues: 136.2900 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 : 0.600 ------------------------------------------------------------------------------- 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: 0.6980 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: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS A 189 HIS A 195 HIS B 22 GLN B 89 HIS B 92 GLN B 274 GLN B 352 GLN C 27 GLN C 180 GLN C 334 HIS C 480 GLN D 22 GLN D 91 GLN D 189 HIS D 199 HIS D 203 HIS 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 = 0.4245 r_free = 0.4245 target = 0.182749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130986 restraints weight = 38110.512| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.68 r_work: 0.3358 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1951 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= 0.184 Angle : 0.705 13.294 28386 Z= 0.398 Chirality : 0.049 0.306 3109 Planarity : 0.005 0.051 3022 Dihedral : 22.905 88.427 4343 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.86 % Allowed : 12.34 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.19), residues: 1937 helix: 2.31 (0.16), residues: 914 sheet: -0.06 (0.27), residues: 287 loop : 0.78 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 181 TYR 0.018 0.002 TYR A 324 PHE 0.025 0.002 PHE D 348 TRP 0.016 0.002 TRP A 64 HIS 0.007 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (20298) covalent geometry : angle 0.68996 / 0.40 (28362) hydrogen bonds : bond 0.05219 / 3.61 ( 1060) hydrogen bonds : angle 3.89758 / 2.80 ( 2790) metal coordination : bond 0.00760 / 0.44 ( 16) metal coordination : angle 5.06679 / 3.22 ( 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 473 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 411 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: symmetry clash revert: 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: 0.6279 (mmm) cc_final: 0.6069 (mmm) REVERT: A 24 GLU cc_start: 0.8570 (tt0) cc_final: 0.8265 (tt0) REVERT: A 28 GLN cc_start: 0.8545 (tt0) cc_final: 0.8306 (tt0) REVERT: A 69 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6126 (mp0) REVERT: A 73 ASP cc_start: 0.6406 (m-30) cc_final: 0.6186 (m-30) REVERT: A 82 ARG cc_start: 0.7894 (mmt180) cc_final: 0.7242 (mmp80) REVERT: A 84 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7472 (m) REVERT: A 86 SER cc_start: 0.8235 (t) cc_final: 0.6973 (p) REVERT: A 88 ARG cc_start: 0.6812 (mtp-110) cc_final: 0.6580 (mtp-110) REVERT: A 98 GLU cc_start: 0.7235 (tp30) cc_final: 0.6871 (tp30) REVERT: A 100 HIS cc_start: 0.7949 (m170) cc_final: 0.7601 (m170) REVERT: A 137 ILE cc_start: 0.8693 (mt) cc_final: 0.8340 (tt) REVERT: A 147 PHE cc_start: 0.8673 (t80) cc_final: 0.8427 (t80) REVERT: A 376 GLU cc_start: 0.8428 (tt0) cc_final: 0.8153 (tt0) REVERT: A 409 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8463 (ptm160) REVERT: A 455 LEU cc_start: 0.8894 (mt) cc_final: 0.8541 (mm) REVERT: A 458 MET cc_start: 0.7749 (mmm) cc_final: 0.6910 (tmm) REVERT: A 481 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: B 1 MET cc_start: 0.7113 (mmm) cc_final: 0.6832 (mmm) REVERT: B 24 GLU cc_start: 0.7429 (tt0) cc_final: 0.7061 (tt0) REVERT: B 79 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7315 (mtm110) REVERT: B 81 ASP cc_start: 0.8353 (p0) cc_final: 0.8139 (p0) REVERT: B 85 ARG cc_start: 0.8280 (mtt90) cc_final: 0.8066 (mtt90) REVERT: B 133 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 135 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 141 ASN cc_start: 0.8682 (m-40) cc_final: 0.8352 (m-40) REVERT: B 143 SER cc_start: 0.8739 (t) cc_final: 0.8512 (m) REVERT: B 153 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8421 (mttm) REVERT: B 155 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8151 (ptt90) REVERT: B 189 HIS cc_start: 0.8239 (m170) cc_final: 0.7791 (m-70) REVERT: B 204 ASP cc_start: 0.7968 (t70) cc_final: 0.7722 (t0) REVERT: B 273 GLU cc_start: 0.8269 (tt0) cc_final: 0.7943 (mm-30) REVERT: B 342 MET cc_start: 0.5296 (ttp) cc_final: 0.4754 (ttp) REVERT: B 348 PHE cc_start: 0.8455 (t80) cc_final: 0.8160 (t80) REVERT: B 458 MET cc_start: 0.8347 (mmt) cc_final: 0.8053 (mmm) REVERT: C 10 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.6631 (t) REVERT: C 21 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7389 (tpp80) REVERT: C 24 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 46 VAL cc_start: 0.8407 (t) cc_final: 0.8162 (p) REVERT: C 54 ASP cc_start: 0.7789 (t0) cc_final: 0.7316 (t70) REVERT: C 69 GLU cc_start: 0.8270 (mp0) cc_final: 0.7685 (mm-30) REVERT: C 88 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7337 (mmm160) REVERT: C 92 GLN cc_start: 0.7994 (mt0) cc_final: 0.7641 (mm-40) REVERT: C 118 PHE cc_start: 0.7700 (p90) cc_final: 0.7427 (p90) REVERT: C 147 PHE cc_start: 0.8622 (t80) cc_final: 0.8384 (t80) REVERT: C 163 TYR cc_start: 0.8363 (m-80) cc_final: 0.8105 (m-80) REVERT: C 186 GLU cc_start: 0.8129 (tp30) cc_final: 0.7631 (tm-30) REVERT: C 199 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6805 (p-80) REVERT: C 208 ARG cc_start: 0.8636 (mpp80) cc_final: 0.8351 (mtm-85) REVERT: C 220 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (tp) REVERT: C 244 MET cc_start: 0.8070 (mmt) cc_final: 0.7822 (mmt) REVERT: C 267 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7531 (mm-30) REVERT: C 279 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7298 (mtt180) REVERT: C 281 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7656 (tp30) REVERT: C 300 ARG cc_start: 0.8394 (mmt180) cc_final: 0.8175 (mmt180) REVERT: C 325 ARG cc_start: 0.6357 (ttp-170) cc_final: 0.5843 (tmm-80) REVERT: C 345 TRP cc_start: 0.7706 (m100) cc_final: 0.7346 (m100) REVERT: C 404 GLU cc_start: 0.8353 (pt0) cc_final: 0.8088 (pp20) REVERT: D 24 GLU cc_start: 0.7719 (tt0) cc_final: 0.7330 (tt0) REVERT: D 27 GLN cc_start: 0.8023 (mt0) cc_final: 0.7751 (mm110) REVERT: D 28 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 69 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7267 (mm-30) REVERT: D 78 TYR cc_start: 0.8528 (t80) cc_final: 0.8231 (t80) REVERT: D 99 ASP cc_start: 0.7852 (m-30) cc_final: 0.7609 (m-30) REVERT: D 154 TYR cc_start: 0.8514 (t80) cc_final: 0.8138 (t80) REVERT: D 182 GLU cc_start: 0.7091 (tt0) cc_final: 0.6603 (tm-30) REVERT: D 186 GLU cc_start: 0.7943 (tt0) cc_final: 0.7728 (tt0) REVERT: D 211 LEU cc_start: 0.8124 (mp) cc_final: 0.7771 (mt) REVERT: D 219 GLN cc_start: 0.7582 (tp-100) cc_final: 0.7226 (tt0) REVERT: D 242 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7861 (mt-10) REVERT: D 247 TYR cc_start: 0.8464 (m-10) cc_final: 0.8237 (m-10) REVERT: D 265 ARG cc_start: 0.8073 (ptt180) cc_final: 0.7778 (ptt180) REVERT: D 302 LEU cc_start: 0.8179 (tp) cc_final: 0.7909 (tp) REVERT: D 309 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6920 (mm-30) REVERT: D 329 MET cc_start: 0.7649 (tpp) cc_final: 0.7360 (tpp) REVERT: D 351 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: D 461 ARG cc_start: 0.6922 (ttm-80) cc_final: 0.6715 (ttm-80) REVERT: D 464 PHE cc_start: 0.6373 (p90) cc_final: 0.5730 (p90) outliers start: 62 outliers final: 31 residues processed: 446 average time/residue: 0.1486 time to fit residues: 96.5492 Evaluate side-chains 433 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 394 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 195 HIS 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 69 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 153 LYS 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 281 GLU 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 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 74 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 220 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: 4.9990 chunk 20 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 148 ASN A 189 HIS A 195 HIS A 274 GLN B 100 HIS B 199 HIS B 274 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN D 22 GLN D 111 HIS D 146 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.177222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125895 restraints weight = 32811.083| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.48 r_work: 0.3290 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 20314 Z= 0.350 Angle : 0.763 13.067 28386 Z= 0.419 Chirality : 0.051 0.286 3109 Planarity : 0.006 0.063 3022 Dihedral : 23.173 84.207 4309 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.86 % Allowed : 14.39 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.19), residues: 1937 helix: 1.92 (0.16), residues: 910 sheet: -0.33 (0.29), residues: 285 loop : 0.48 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 325 TYR 0.027 0.003 TYR C 154 PHE 0.038 0.003 PHE C 476 TRP 0.025 0.002 TRP C 172 HIS 0.028 0.002 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.35 (20298) covalent geometry : angle 0.75192 / 0.42 (28362) hydrogen bonds : bond 0.05930 / 4.11 ( 1060) hydrogen bonds : angle 4.05010 / 2.91 ( 2790) metal coordination : bond 0.01413 / 0.82 ( 16) metal coordination : angle 4.50517 / 2.81 ( 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 474 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 412 time to evaluate : 0.630 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: A 1 MET cc_start: 0.6286 (mmm) cc_final: 0.6014 (mmm) REVERT: A 28 GLN cc_start: 0.8573 (tt0) cc_final: 0.8276 (tt0) REVERT: A 73 ASP cc_start: 0.6668 (m-30) cc_final: 0.6460 (m-30) REVERT: A 82 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7509 (mmp80) REVERT: A 84 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 98 GLU cc_start: 0.7527 (tp30) cc_final: 0.7112 (tp30) REVERT: A 100 HIS cc_start: 0.8112 (m170) cc_final: 0.7788 (m170) REVERT: A 137 ILE cc_start: 0.8682 (mt) cc_final: 0.8375 (tt) REVERT: A 147 PHE cc_start: 0.8756 (t80) cc_final: 0.8529 (t80) REVERT: A 182 GLU cc_start: 0.7654 (tt0) cc_final: 0.7387 (tt0) REVERT: A 200 LEU cc_start: 0.8299 (mt) cc_final: 0.7970 (mt) REVERT: A 203 HIS cc_start: 0.7967 (t-90) cc_final: 0.7535 (t-90) REVERT: A 219 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7468 (mm-40) REVERT: A 220 LEU cc_start: 0.8438 (mt) cc_final: 0.8134 (mt) REVERT: A 355 ASP cc_start: 0.8546 (m-30) cc_final: 0.8308 (p0) REVERT: A 376 GLU cc_start: 0.8534 (tt0) cc_final: 0.8320 (tt0) REVERT: A 383 GLU cc_start: 0.9017 (tt0) cc_final: 0.8574 (tt0) REVERT: A 391 ILE cc_start: 0.6832 (mt) cc_final: 0.6575 (mt) REVERT: A 409 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8427 (ptm160) REVERT: A 455 LEU cc_start: 0.9016 (mt) cc_final: 0.8426 (mm) REVERT: A 458 MET cc_start: 0.8164 (mmm) cc_final: 0.7702 (tmm) REVERT: A 481 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: B 1 MET cc_start: 0.7761 (mmm) cc_final: 0.7417 (mmm) REVERT: B 7 ILE cc_start: 0.8069 (mm) cc_final: 0.7745 (mm) REVERT: B 43 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: B 79 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7860 (mtm110) REVERT: B 133 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7985 (mt-10) REVERT: B 135 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8243 (mm-30) REVERT: B 141 ASN cc_start: 0.8715 (m-40) cc_final: 0.8315 (m-40) REVERT: B 143 SER cc_start: 0.8742 (t) cc_final: 0.8539 (m) REVERT: B 155 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8257 (ptt90) REVERT: B 189 HIS cc_start: 0.8521 (m170) cc_final: 0.8095 (m-70) REVERT: B 204 ASP cc_start: 0.8255 (t70) cc_final: 0.8042 (t0) REVERT: B 221 GLN cc_start: 0.7981 (mm110) cc_final: 0.7589 (mm110) REVERT: B 273 GLU cc_start: 0.8547 (tt0) cc_final: 0.8337 (tt0) REVERT: B 342 MET cc_start: 0.5510 (ttp) cc_final: 0.5004 (ttp) REVERT: B 348 PHE cc_start: 0.8618 (t80) cc_final: 0.8336 (t80) REVERT: B 375 VAL cc_start: 0.8529 (p) cc_final: 0.8267 (m) REVERT: B 443 TRP cc_start: 0.7964 (t-100) cc_final: 0.7389 (t-100) REVERT: B 458 MET cc_start: 0.8453 (mmt) cc_final: 0.8187 (mmm) REVERT: C 21 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7858 (tpp80) REVERT: C 24 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 46 VAL cc_start: 0.8709 (t) cc_final: 0.8461 (p) REVERT: C 54 ASP cc_start: 0.8171 (t0) cc_final: 0.7544 (t70) REVERT: C 56 LYS cc_start: 0.8060 (tppp) cc_final: 0.7699 (tppp) REVERT: C 79 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7838 (mtp85) REVERT: C 81 ASP cc_start: 0.8181 (p0) cc_final: 0.7941 (p0) REVERT: C 92 GLN cc_start: 0.8487 (mt0) cc_final: 0.8272 (mt0) REVERT: C 116 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8588 (p) REVERT: C 118 PHE cc_start: 0.7974 (p90) cc_final: 0.7700 (p90) REVERT: C 132 MET cc_start: 0.8435 (mmm) cc_final: 0.8156 (mtp) REVERT: C 135 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8371 (mm-30) REVERT: C 140 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (mtt90) REVERT: C 147 PHE cc_start: 0.8808 (t80) cc_final: 0.8577 (t80) REVERT: C 163 TYR cc_start: 0.8802 (m-80) cc_final: 0.8516 (m-80) REVERT: C 177 ASP cc_start: 0.7606 (t0) cc_final: 0.7367 (t0) REVERT: C 186 GLU cc_start: 0.8281 (tp30) cc_final: 0.7724 (tp30) REVERT: C 199 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.6968 (p-80) REVERT: C 208 ARG cc_start: 0.8776 (mpp80) cc_final: 0.8498 (mtm-85) REVERT: C 220 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8609 (tp) REVERT: C 242 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7777 (mt-10) REVERT: C 279 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7657 (mtt180) REVERT: C 281 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7680 (tp30) REVERT: C 300 ARG cc_start: 0.8452 (mmt180) cc_final: 0.8251 (mmt180) REVERT: C 309 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7071 (mp0) REVERT: C 342 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4264 (mmm) REVERT: C 433 ARG cc_start: 0.7411 (tpt-90) cc_final: 0.7182 (mmm160) REVERT: D 27 GLN cc_start: 0.8322 (mt0) cc_final: 0.8050 (mm110) REVERT: D 28 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7553 (tm-30) REVERT: D 32 GLN cc_start: 0.8118 (tp40) cc_final: 0.7914 (tp40) REVERT: D 78 TYR cc_start: 0.8656 (t80) cc_final: 0.8306 (t80) REVERT: D 109 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7624 (mt-10) REVERT: D 179 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7521 (p) REVERT: D 182 GLU cc_start: 0.7634 (tt0) cc_final: 0.6997 (tm-30) REVERT: D 186 GLU cc_start: 0.8109 (tt0) cc_final: 0.7863 (tt0) REVERT: D 204 ASP cc_start: 0.8205 (t70) cc_final: 0.7886 (t0) REVERT: D 211 LEU cc_start: 0.8481 (mp) cc_final: 0.8124 (mt) REVERT: D 219 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7637 (tt0) REVERT: D 265 ARG cc_start: 0.8497 (ptt180) cc_final: 0.8228 (ptt180) REVERT: D 309 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7520 (mm-30) REVERT: D 329 MET cc_start: 0.8070 (tpp) cc_final: 0.7784 (tpp) REVERT: D 348 PHE cc_start: 0.8101 (t80) cc_final: 0.7641 (t80) REVERT: D 351 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: D 464 PHE cc_start: 0.6598 (p90) cc_final: 0.6158 (p90) outliers start: 62 outliers final: 40 residues processed: 442 average time/residue: 0.1728 time to fit residues: 110.8235 Evaluate side-chains 457 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 406 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 92 GLN 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 281 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 371 SER 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 140 ARG Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 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 486 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 179 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 36 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 133 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS A 226 GLN A 274 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 274 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.179153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126686 restraints weight = 44187.822| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.93 r_work: 0.3283 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 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 = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20314 Z= 0.199 Angle : 0.620 8.509 28386 Z= 0.350 Chirality : 0.043 0.215 3109 Planarity : 0.005 0.045 3022 Dihedral : 23.237 85.637 4304 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.05 % Allowed : 15.02 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1937 helix: 2.24 (0.16), residues: 912 sheet: -0.18 (0.30), residues: 282 loop : 0.55 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 150 TYR 0.018 0.002 TYR B 154 PHE 0.021 0.002 PHE C 314 TRP 0.019 0.001 TRP D 96 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (20298) covalent geometry : angle 0.60991 / 0.35 (28362) hydrogen bonds : bond 0.04741 / 3.29 ( 1060) hydrogen bonds : angle 3.81046 / 2.73 ( 2790) metal coordination : bond 0.00696 / 0.41 ( 16) metal coordination : angle 3.80184 / 2.34 ( 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 473 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 408 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8593 (tt0) cc_final: 0.8269 (tt0) REVERT: A 82 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7477 (mmp80) REVERT: A 84 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7846 (m) REVERT: A 98 GLU cc_start: 0.7353 (tp30) cc_final: 0.6933 (tp30) REVERT: A 100 HIS cc_start: 0.8016 (m170) cc_final: 0.7696 (m170) REVERT: A 137 ILE cc_start: 0.8574 (mt) cc_final: 0.8292 (tt) REVERT: A 147 PHE cc_start: 0.8655 (t80) cc_final: 0.8393 (t80) REVERT: A 155 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7516 (ptt90) REVERT: A 182 GLU cc_start: 0.7315 (tt0) cc_final: 0.7062 (tt0) REVERT: A 203 HIS cc_start: 0.7763 (t-90) cc_final: 0.7303 (t-90) REVERT: A 205 LEU cc_start: 0.8527 (mp) cc_final: 0.8319 (mm) REVERT: A 219 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7270 (mm-40) REVERT: A 220 LEU cc_start: 0.8372 (mt) cc_final: 0.7982 (tt) REVERT: A 376 GLU cc_start: 0.8461 (tt0) cc_final: 0.8240 (tt0) REVERT: A 383 GLU cc_start: 0.8941 (tt0) cc_final: 0.8452 (tt0) REVERT: A 391 ILE cc_start: 0.6694 (mt) cc_final: 0.6445 (mt) REVERT: A 409 ARG cc_start: 0.8727 (ttp-170) cc_final: 0.8434 (ptm160) REVERT: A 455 LEU cc_start: 0.8953 (mt) cc_final: 0.8342 (mm) REVERT: A 458 MET cc_start: 0.8100 (mmm) cc_final: 0.7622 (tmm) REVERT: A 481 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: B 7 ILE cc_start: 0.7905 (mm) cc_final: 0.7118 (mm) REVERT: B 42 GLU cc_start: 0.7461 (tp30) cc_final: 0.7249 (tp30) REVERT: B 43 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: B 68 GLU cc_start: 0.6824 (pt0) cc_final: 0.6400 (pp20) REVERT: B 79 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7351 (mtm110) REVERT: B 133 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 135 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 141 ASN cc_start: 0.8618 (m-40) cc_final: 0.8243 (m-40) REVERT: B 143 SER cc_start: 0.8630 (t) cc_final: 0.8401 (m) REVERT: B 155 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8056 (ptt180) REVERT: B 189 HIS cc_start: 0.8311 (m170) cc_final: 0.7883 (m-70) REVERT: B 221 GLN cc_start: 0.7819 (mm110) cc_final: 0.7407 (mm110) REVERT: B 284 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8030 (mtmm) REVERT: B 342 MET cc_start: 0.5252 (ttp) cc_final: 0.4752 (ttp) REVERT: B 348 PHE cc_start: 0.8588 (t80) cc_final: 0.8288 (t80) REVERT: B 371 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 443 TRP cc_start: 0.7770 (t-100) cc_final: 0.7256 (t-100) REVERT: B 458 MET cc_start: 0.8355 (mmt) cc_final: 0.8063 (mmm) REVERT: C 10 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7242 (t) REVERT: C 21 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7699 (tpp80) REVERT: C 24 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 46 VAL cc_start: 0.8637 (t) cc_final: 0.8402 (p) REVERT: C 54 ASP cc_start: 0.8055 (t0) cc_final: 0.7578 (t0) REVERT: C 56 LYS cc_start: 0.7945 (tppp) cc_final: 0.7701 (tppp) REVERT: C 57 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7117 (mmt90) REVERT: C 69 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: C 92 GLN cc_start: 0.8263 (mt0) cc_final: 0.8023 (mt0) REVERT: C 99 ASP cc_start: 0.7113 (m-30) cc_final: 0.6868 (m-30) REVERT: C 118 PHE cc_start: 0.7758 (p90) cc_final: 0.7444 (p90) REVERT: C 132 MET cc_start: 0.8166 (mmm) cc_final: 0.7880 (mtp) REVERT: C 135 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 142 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8003 (ttp-110) REVERT: C 147 PHE cc_start: 0.8743 (t80) cc_final: 0.8450 (t80) REVERT: C 163 TYR cc_start: 0.8758 (m-80) cc_final: 0.8409 (m-80) REVERT: C 186 GLU cc_start: 0.8140 (tp30) cc_final: 0.7788 (tp30) REVERT: C 199 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6847 (p-80) REVERT: C 208 ARG cc_start: 0.8612 (mpp80) cc_final: 0.7918 (mpp80) REVERT: C 267 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7925 (mm-30) REVERT: C 278 LEU cc_start: 0.8042 (mt) cc_final: 0.7840 (mm) REVERT: C 279 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7436 (mtt180) REVERT: C 281 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7885 (tp30) REVERT: C 300 ARG cc_start: 0.8364 (mmt180) cc_final: 0.8108 (mmt-90) REVERT: C 309 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6929 (mp0) REVERT: C 342 MET cc_start: 0.4779 (OUTLIER) cc_final: 0.4026 (mmm) REVERT: C 433 ARG cc_start: 0.7406 (tpt-90) cc_final: 0.7176 (mmm160) REVERT: C 459 ASN cc_start: 0.8403 (m-40) cc_final: 0.8008 (m110) REVERT: D 27 GLN cc_start: 0.8158 (mt0) cc_final: 0.7898 (mm110) REVERT: D 28 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7323 (tm-30) REVERT: D 32 GLN cc_start: 0.7925 (tp40) cc_final: 0.7710 (tp40) REVERT: D 78 TYR cc_start: 0.8540 (t80) cc_final: 0.8230 (t80) REVERT: D 109 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7442 (mt-10) REVERT: D 154 TYR cc_start: 0.8510 (t80) cc_final: 0.8136 (t80) REVERT: D 179 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7341 (p) REVERT: D 182 GLU cc_start: 0.7322 (tt0) cc_final: 0.6760 (tm-30) REVERT: D 186 GLU cc_start: 0.7956 (tt0) cc_final: 0.7686 (tt0) REVERT: D 204 ASP cc_start: 0.8020 (t70) cc_final: 0.7650 (t0) REVERT: D 211 LEU cc_start: 0.8339 (mp) cc_final: 0.8021 (mt) REVERT: D 219 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7404 (tt0) REVERT: D 265 ARG cc_start: 0.8389 (ptt180) cc_final: 0.8158 (ptt180) REVERT: D 329 MET cc_start: 0.7918 (tpp) cc_final: 0.7580 (tpp) REVERT: D 351 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7541 (pt0) REVERT: D 464 PHE cc_start: 0.6443 (p90) cc_final: 0.6116 (p90) outliers start: 65 outliers final: 43 residues processed: 439 average time/residue: 0.1687 time to fit residues: 106.8517 Evaluate side-chains 459 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 403 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 101 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU 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 283 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 371 SER 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 74 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 350 GLU 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 7 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 179 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 148 ASN B 199 HIS B 274 GLN C 27 GLN D 22 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.180634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129562 restraints weight = 34256.898| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.54 r_work: 0.3342 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20314 Z= 0.148 Angle : 0.581 8.236 28386 Z= 0.329 Chirality : 0.041 0.179 3109 Planarity : 0.005 0.053 3022 Dihedral : 23.212 87.617 4298 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.99 % Allowed : 15.14 % 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: 1.99 (0.20), residues: 1937 helix: 2.43 (0.17), residues: 913 sheet: -0.21 (0.29), residues: 291 loop : 0.69 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 409 TYR 0.017 0.002 TYR D 188 PHE 0.029 0.001 PHE C 314 TRP 0.022 0.001 TRP A 64 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (20298) covalent geometry : angle 0.57267 / 0.33 (28362) hydrogen bonds : bond 0.04284 / 2.97 ( 1060) hydrogen bonds : angle 3.68834 / 2.63 ( 2790) metal coordination : bond 0.00448 / 0.28 ( 16) metal coordination : angle 3.41128 / 2.10 ( 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 478 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 414 time to evaluate : 0.632 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: A 1 MET cc_start: 0.6542 (mmm) cc_final: 0.6081 (mmm) REVERT: A 28 GLN cc_start: 0.8551 (tt0) cc_final: 0.8267 (tt0) REVERT: A 69 GLU cc_start: 0.6477 (mp0) cc_final: 0.6192 (mp0) REVERT: A 82 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7349 (mmp80) REVERT: A 84 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7819 (m) REVERT: A 98 GLU cc_start: 0.7327 (tp30) cc_final: 0.6854 (tp30) REVERT: A 100 HIS cc_start: 0.7965 (m170) cc_final: 0.7643 (m170) REVERT: A 137 ILE cc_start: 0.8558 (mt) cc_final: 0.8283 (tt) REVERT: A 147 PHE cc_start: 0.8648 (t80) cc_final: 0.8368 (t80) REVERT: A 155 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7554 (ptt90) REVERT: A 182 GLU cc_start: 0.7187 (tt0) cc_final: 0.6934 (tt0) REVERT: A 200 LEU cc_start: 0.8128 (mt) cc_final: 0.7831 (mt) REVERT: A 203 HIS cc_start: 0.7656 (t-90) cc_final: 0.7182 (t-90) REVERT: A 205 LEU cc_start: 0.8553 (mp) cc_final: 0.8350 (mm) REVERT: A 219 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7221 (mm-40) REVERT: A 220 LEU cc_start: 0.8329 (mt) cc_final: 0.7985 (tt) REVERT: A 376 GLU cc_start: 0.8424 (tt0) cc_final: 0.8195 (tt0) REVERT: A 383 GLU cc_start: 0.8877 (tt0) cc_final: 0.8440 (tt0) REVERT: A 391 ILE cc_start: 0.6586 (mt) cc_final: 0.6335 (mt) REVERT: A 407 ASP cc_start: 0.8181 (m-30) cc_final: 0.7954 (m-30) REVERT: A 409 ARG cc_start: 0.8708 (ttp-170) cc_final: 0.8397 (ptm160) REVERT: A 455 LEU cc_start: 0.8955 (mt) cc_final: 0.8407 (mm) REVERT: A 458 MET cc_start: 0.8023 (mmm) cc_final: 0.7460 (tmm) REVERT: A 481 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: B 7 ILE cc_start: 0.7919 (mm) cc_final: 0.7148 (mm) REVERT: B 43 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: B 79 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7296 (mtm110) REVERT: B 133 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 135 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 141 ASN cc_start: 0.8585 (m-40) cc_final: 0.8236 (m-40) REVERT: B 143 SER cc_start: 0.8628 (t) cc_final: 0.8414 (m) REVERT: B 155 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8050 (ppt170) REVERT: B 189 HIS cc_start: 0.8239 (m170) cc_final: 0.7937 (m-70) REVERT: B 221 GLN cc_start: 0.7755 (mm110) cc_final: 0.7359 (mm110) REVERT: B 273 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: B 284 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8079 (mtmm) REVERT: B 342 MET cc_start: 0.4867 (ttp) cc_final: 0.4433 (ttp) REVERT: B 348 PHE cc_start: 0.8641 (t80) cc_final: 0.8358 (t80) REVERT: B 371 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 458 MET cc_start: 0.8322 (mmt) cc_final: 0.7843 (mmp) REVERT: C 10 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.6687 (t) REVERT: C 21 ARG cc_start: 0.7840 (mmm160) cc_final: 0.7538 (tpp80) REVERT: C 24 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 46 VAL cc_start: 0.8616 (t) cc_final: 0.8383 (p) REVERT: C 54 ASP cc_start: 0.8038 (t0) cc_final: 0.7563 (t0) REVERT: C 56 LYS cc_start: 0.7902 (tppp) cc_final: 0.7671 (tppp) REVERT: C 57 ARG cc_start: 0.7474 (mmt90) cc_final: 0.7114 (mmt90) REVERT: C 69 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: C 92 GLN cc_start: 0.8199 (mt0) cc_final: 0.7974 (mt0) REVERT: C 99 ASP cc_start: 0.7015 (m-30) cc_final: 0.6717 (m-30) REVERT: C 135 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7999 (mm-30) REVERT: C 142 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7974 (ttp-110) REVERT: C 147 PHE cc_start: 0.8730 (t80) cc_final: 0.8390 (t80) REVERT: C 163 TYR cc_start: 0.8730 (m-80) cc_final: 0.8344 (m-80) REVERT: C 186 GLU cc_start: 0.8086 (tp30) cc_final: 0.7660 (tm-30) REVERT: C 199 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6806 (p-80) REVERT: C 204 ASP cc_start: 0.8011 (t70) cc_final: 0.7258 (t70) REVERT: C 208 ARG cc_start: 0.8359 (mpp80) cc_final: 0.7871 (mpp80) REVERT: C 220 LEU cc_start: 0.8778 (tt) cc_final: 0.8451 (tt) REVERT: C 228 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7694 (mtm-85) REVERT: C 241 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.7053 (p) REVERT: C 267 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 279 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7410 (mtt180) REVERT: C 281 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7862 (tp30) REVERT: C 300 ARG cc_start: 0.8398 (mmt180) cc_final: 0.8119 (mmt-90) REVERT: C 309 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6895 (mp0) REVERT: C 325 ARG cc_start: 0.6697 (tmm-80) cc_final: 0.6381 (ttp80) REVERT: C 342 MET cc_start: 0.4653 (OUTLIER) cc_final: 0.3898 (mmm) REVERT: C 433 ARG cc_start: 0.7366 (tpt-90) cc_final: 0.7121 (mmm160) REVERT: C 459 ASN cc_start: 0.8368 (m-40) cc_final: 0.7999 (m110) REVERT: D 27 GLN cc_start: 0.8126 (mt0) cc_final: 0.7923 (mm110) REVERT: D 28 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 32 GLN cc_start: 0.7864 (tp40) cc_final: 0.7627 (tp40) REVERT: D 42 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: D 78 TYR cc_start: 0.8518 (t80) cc_final: 0.8189 (t80) REVERT: D 109 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7404 (mt-10) REVERT: D 154 TYR cc_start: 0.8477 (t80) cc_final: 0.8120 (t80) REVERT: D 173 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7818 (mtp180) REVERT: D 179 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7184 (p) REVERT: D 182 GLU cc_start: 0.7159 (tt0) cc_final: 0.6618 (tm-30) REVERT: D 186 GLU cc_start: 0.7895 (tt0) cc_final: 0.7656 (tt0) REVERT: D 204 ASP cc_start: 0.7980 (t70) cc_final: 0.7573 (t0) REVERT: D 219 GLN cc_start: 0.7640 (tp-100) cc_final: 0.7332 (tt0) REVERT: D 247 TYR cc_start: 0.8519 (m-10) cc_final: 0.8261 (m-10) REVERT: D 329 MET cc_start: 0.7817 (tpp) cc_final: 0.7527 (tpp) REVERT: D 351 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: D 464 PHE cc_start: 0.6365 (p90) cc_final: 0.6055 (p90) outliers start: 64 outliers final: 42 residues processed: 448 average time/residue: 0.1777 time to fit residues: 114.7895 Evaluate side-chains 460 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 402 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 101 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU 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 273 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 371 SER 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 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 199 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 241 SER 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 461 ARG Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 179 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 146 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 274 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS D 22 GLN D 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.176434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124631 restraints weight = 36687.190| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.66 r_work: 0.3262 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 20314 Z= 0.367 Angle : 0.736 10.498 28386 Z= 0.405 Chirality : 0.049 0.295 3109 Planarity : 0.006 0.077 3022 Dihedral : 23.352 88.260 4296 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.12 % Favored : 97.83 % Rotamer: Outliers : 4.49 % Allowed : 16.20 % 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: 1.35 (0.19), residues: 1937 helix: 1.82 (0.16), residues: 913 sheet: -0.27 (0.29), residues: 294 loop : 0.35 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 409 TYR 0.030 0.003 TYR B 163 PHE 0.037 0.002 PHE C 118 TRP 0.020 0.002 TRP D 96 HIS 0.015 0.002 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.37 (20298) covalent geometry : angle 0.72757 / 0.40 (28362) hydrogen bonds : bond 0.05778 / 4.01 ( 1060) hydrogen bonds : angle 3.98419 / 2.86 ( 2790) metal coordination : bond 0.01363 / 0.81 ( 16) metal coordination : angle 3.81545 / 2.26 ( 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 500 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 428 time to evaluate : 0.632 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: A 1 MET cc_start: 0.6420 (mmm) cc_final: 0.6184 (mmm) REVERT: A 27 GLN cc_start: 0.7880 (mt0) cc_final: 0.7484 (mt0) REVERT: A 28 GLN cc_start: 0.8541 (tt0) cc_final: 0.8256 (tt0) REVERT: A 82 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7428 (mmp80) REVERT: A 98 GLU cc_start: 0.7399 (tp30) cc_final: 0.6909 (tp30) REVERT: A 100 HIS cc_start: 0.7981 (m170) cc_final: 0.7623 (m170) REVERT: A 113 ASP cc_start: 0.7360 (t0) cc_final: 0.7126 (t70) REVERT: A 116 THR cc_start: 0.6532 (OUTLIER) cc_final: 0.5744 (p) REVERT: A 137 ILE cc_start: 0.8510 (mt) cc_final: 0.8256 (tt) REVERT: A 147 PHE cc_start: 0.8634 (t80) cc_final: 0.8419 (t80) REVERT: A 155 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7543 (ptt90) REVERT: A 164 LEU cc_start: 0.8295 (mm) cc_final: 0.8079 (mt) REVERT: A 182 GLU cc_start: 0.7513 (tt0) cc_final: 0.7240 (tt0) REVERT: A 203 HIS cc_start: 0.7756 (t-90) cc_final: 0.7296 (t-90) REVERT: A 205 LEU cc_start: 0.8581 (mp) cc_final: 0.8378 (mm) REVERT: A 342 MET cc_start: 0.5214 (ttp) cc_final: 0.4936 (ttp) REVERT: A 376 GLU cc_start: 0.8437 (tt0) cc_final: 0.8226 (tt0) REVERT: A 383 GLU cc_start: 0.8904 (tt0) cc_final: 0.8486 (tt0) REVERT: A 391 ILE cc_start: 0.6721 (mt) cc_final: 0.6504 (mt) REVERT: A 407 ASP cc_start: 0.8153 (m-30) cc_final: 0.7910 (m-30) REVERT: A 409 ARG cc_start: 0.8750 (ttp-170) cc_final: 0.8451 (ptm160) REVERT: A 455 LEU cc_start: 0.9029 (mt) cc_final: 0.8560 (mm) REVERT: A 458 MET cc_start: 0.8220 (mmm) cc_final: 0.7330 (tmm) REVERT: A 481 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: B 7 ILE cc_start: 0.8023 (mm) cc_final: 0.7546 (mm) REVERT: B 42 GLU cc_start: 0.7041 (tp30) cc_final: 0.6809 (tp30) REVERT: B 43 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6348 (m-30) REVERT: B 51 ASP cc_start: 0.8319 (t0) cc_final: 0.8024 (t0) REVERT: B 79 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7459 (mtm180) REVERT: B 86 SER cc_start: 0.8992 (t) cc_final: 0.8483 (p) REVERT: B 133 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 135 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 141 ASN cc_start: 0.8579 (m-40) cc_final: 0.8303 (m-40) REVERT: B 155 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8406 (ptt180) REVERT: B 284 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8080 (mtmm) REVERT: B 342 MET cc_start: 0.5278 (ttp) cc_final: 0.4803 (ttp) REVERT: B 345 TRP cc_start: 0.6967 (m100) cc_final: 0.6723 (m100) REVERT: B 443 TRP cc_start: 0.7817 (t-100) cc_final: 0.7240 (t-100) REVERT: B 458 MET cc_start: 0.8260 (mmt) cc_final: 0.7813 (mmp) REVERT: C 10 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.7442 (t) REVERT: C 21 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7715 (tpp80) REVERT: C 24 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 46 VAL cc_start: 0.8670 (t) cc_final: 0.8438 (p) REVERT: C 54 ASP cc_start: 0.8109 (t0) cc_final: 0.7609 (t0) REVERT: C 56 LYS cc_start: 0.7952 (tppp) cc_final: 0.7743 (tppp) REVERT: C 57 ARG cc_start: 0.7558 (mmt90) cc_final: 0.7216 (mmt90) REVERT: C 69 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: C 92 GLN cc_start: 0.8296 (mt0) cc_final: 0.8054 (mt0) REVERT: C 132 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7908 (mtp) REVERT: C 135 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 147 PHE cc_start: 0.8777 (t80) cc_final: 0.8475 (t80) REVERT: C 177 ASP cc_start: 0.7446 (t0) cc_final: 0.7170 (t0) REVERT: C 186 GLU cc_start: 0.8108 (tp30) cc_final: 0.7793 (tp30) REVERT: C 199 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.6984 (p-80) REVERT: C 208 ARG cc_start: 0.8261 (mpp80) cc_final: 0.7793 (mpp80) REVERT: C 220 LEU cc_start: 0.8793 (tt) cc_final: 0.8479 (tt) REVERT: C 279 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7472 (mtt180) REVERT: C 281 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7829 (tp30) REVERT: C 300 ARG cc_start: 0.8442 (mmt180) cc_final: 0.8196 (mmt-90) REVERT: C 309 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7065 (mp0) REVERT: C 342 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4061 (mmm) REVERT: C 433 ARG cc_start: 0.7520 (tpt-90) cc_final: 0.7131 (mmm160) REVERT: C 459 ASN cc_start: 0.8612 (m-40) cc_final: 0.8277 (m110) REVERT: D 20 GLU cc_start: 0.7667 (mp0) cc_final: 0.7140 (mp0) REVERT: D 22 GLN cc_start: 0.8200 (mt0) cc_final: 0.7994 (mt0) REVERT: D 28 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7304 (tm-30) REVERT: D 32 GLN cc_start: 0.7956 (tp40) cc_final: 0.7678 (tp40) REVERT: D 42 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: D 78 TYR cc_start: 0.8510 (t80) cc_final: 0.8178 (t80) REVERT: D 81 ASP cc_start: 0.8318 (p0) cc_final: 0.8021 (p0) REVERT: D 109 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7440 (mt-10) REVERT: D 179 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7569 (p) REVERT: D 182 GLU cc_start: 0.7352 (tt0) cc_final: 0.6776 (tm-30) REVERT: D 186 GLU cc_start: 0.7911 (tt0) cc_final: 0.7703 (tt0) REVERT: D 219 GLN cc_start: 0.7715 (tp-100) cc_final: 0.7358 (tt0) REVERT: D 329 MET cc_start: 0.7996 (tpp) cc_final: 0.7702 (tpp) REVERT: D 345 TRP cc_start: 0.7662 (m100) cc_final: 0.7411 (m100) REVERT: D 351 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: D 409 ARG cc_start: 0.8842 (mmm160) cc_final: 0.8505 (mmm160) REVERT: D 464 PHE cc_start: 0.6503 (p90) cc_final: 0.6209 (p90) outliers start: 72 outliers final: 50 residues processed: 464 average time/residue: 0.1654 time to fit residues: 110.7211 Evaluate side-chains 470 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 407 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU 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 200 LEU Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 339 THR 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 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 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 132 MET Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 SER 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 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 179 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 133 optimal weight: 50.0000 chunk 138 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 91 GLN B 199 HIS B 274 GLN B 352 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.179476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128792 restraints weight = 31553.789| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.42 r_work: 0.3342 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3559 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= 0.144 Angle : 0.606 8.373 28386 Z= 0.339 Chirality : 0.042 0.193 3109 Planarity : 0.005 0.044 3022 Dihedral : 23.299 86.993 4296 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.60 % Favored : 98.35 % Rotamer: Outliers : 3.80 % Allowed : 18.38 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 1937 helix: 2.22 (0.17), residues: 913 sheet: -0.21 (0.29), residues: 295 loop : 0.49 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 223 TYR 0.023 0.002 TYR C 396 PHE 0.038 0.002 PHE C 314 TRP 0.023 0.001 TRP A 64 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (20298) covalent geometry : angle 0.59670 / 0.34 (28362) hydrogen bonds : bond 0.04385 / 3.04 ( 1060) hydrogen bonds : angle 3.73136 / 2.67 ( 2790) metal coordination : bond 0.00503 / 0.31 ( 16) metal coordination : angle 3.62790 / 2.16 ( 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 465 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 404 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6677 (mmm) cc_final: 0.6435 (mmm) REVERT: A 27 GLN cc_start: 0.7927 (mt0) cc_final: 0.7632 (mt0) REVERT: A 28 GLN cc_start: 0.8553 (tt0) cc_final: 0.8254 (tt0) REVERT: A 64 TRP cc_start: 0.8236 (m-10) cc_final: 0.7965 (m-10) REVERT: A 69 GLU cc_start: 0.6533 (mp0) cc_final: 0.6242 (mp0) REVERT: A 82 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7415 (mmp80) REVERT: A 84 THR cc_start: 0.8132 (m) cc_final: 0.7905 (m) REVERT: A 98 GLU cc_start: 0.7463 (tp30) cc_final: 0.7008 (tp30) REVERT: A 100 HIS cc_start: 0.8103 (m170) cc_final: 0.7771 (m170) REVERT: A 113 ASP cc_start: 0.7286 (t0) cc_final: 0.7067 (t70) REVERT: A 137 ILE cc_start: 0.8646 (mt) cc_final: 0.8380 (tt) REVERT: A 147 PHE cc_start: 0.8802 (t80) cc_final: 0.8571 (t80) REVERT: A 155 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7519 (ptt90) REVERT: A 182 GLU cc_start: 0.7618 (tt0) cc_final: 0.7348 (tt0) REVERT: A 200 LEU cc_start: 0.8199 (mt) cc_final: 0.7938 (mt) REVERT: A 203 HIS cc_start: 0.7888 (t-90) cc_final: 0.7411 (t-90) REVERT: A 205 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8353 (mm) REVERT: A 342 MET cc_start: 0.5294 (ttp) cc_final: 0.5010 (ttp) REVERT: A 376 GLU cc_start: 0.8448 (tt0) cc_final: 0.8235 (tt0) REVERT: A 383 GLU cc_start: 0.8929 (tt0) cc_final: 0.8540 (tt0) REVERT: A 407 ASP cc_start: 0.8181 (m-30) cc_final: 0.7930 (m-30) REVERT: A 409 ARG cc_start: 0.8692 (ttp-170) cc_final: 0.8399 (ptm160) REVERT: A 455 LEU cc_start: 0.9046 (mt) cc_final: 0.8722 (mp) REVERT: A 458 MET cc_start: 0.8134 (mmm) cc_final: 0.7153 (tmm) REVERT: A 481 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: B 7 ILE cc_start: 0.8045 (mm) cc_final: 0.7615 (mm) REVERT: B 42 GLU cc_start: 0.7138 (tp30) cc_final: 0.6902 (tp30) REVERT: B 43 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6543 (m-30) REVERT: B 51 ASP cc_start: 0.8315 (t0) cc_final: 0.8109 (t0) REVERT: B 79 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7476 (mtm110) REVERT: B 133 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 135 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B 141 ASN cc_start: 0.8653 (m-40) cc_final: 0.8298 (m-40) REVERT: B 143 SER cc_start: 0.8688 (t) cc_final: 0.8481 (m) REVERT: B 155 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8139 (ptt180) REVERT: B 273 GLU cc_start: 0.8486 (tt0) cc_final: 0.8134 (mm-30) REVERT: B 281 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7758 (tp30) REVERT: B 284 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8116 (mtmm) REVERT: B 342 MET cc_start: 0.5171 (ttp) cc_final: 0.4728 (ttp) REVERT: B 345 TRP cc_start: 0.6940 (m100) cc_final: 0.6703 (m100) REVERT: B 371 SER cc_start: 0.8558 (t) cc_final: 0.8322 (p) REVERT: B 379 GLU cc_start: 0.8609 (pt0) cc_final: 0.8245 (pp20) REVERT: B 443 TRP cc_start: 0.7934 (t-100) cc_final: 0.7329 (t-100) REVERT: B 458 MET cc_start: 0.8327 (mmt) cc_final: 0.7889 (mmp) REVERT: C 10 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7129 (t) REVERT: C 21 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7771 (tpp80) REVERT: C 24 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 46 VAL cc_start: 0.8658 (t) cc_final: 0.8444 (p) REVERT: C 69 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: C 92 GLN cc_start: 0.8525 (mt0) cc_final: 0.8253 (mt0) REVERT: C 135 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8325 (mm-30) REVERT: C 142 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8207 (ttp-110) REVERT: C 147 PHE cc_start: 0.8838 (t80) cc_final: 0.8542 (t80) REVERT: C 177 ASP cc_start: 0.7746 (t0) cc_final: 0.7434 (t0) REVERT: C 186 GLU cc_start: 0.8180 (tp30) cc_final: 0.7787 (tm-30) REVERT: C 187 VAL cc_start: 0.8216 (t) cc_final: 0.7958 (p) REVERT: C 199 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6939 (p-80) REVERT: C 204 ASP cc_start: 0.8319 (t70) cc_final: 0.8056 (t70) REVERT: C 208 ARG cc_start: 0.8526 (mpp80) cc_final: 0.8153 (mpp80) REVERT: C 228 ARG cc_start: 0.8313 (mtm180) cc_final: 0.7980 (mtm-85) REVERT: C 240 ILE cc_start: 0.8437 (mm) cc_final: 0.7781 (tt) REVERT: C 279 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7658 (mtt180) REVERT: C 281 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7999 (tp30) REVERT: C 300 ARG cc_start: 0.8326 (mmt180) cc_final: 0.8105 (mmt-90) REVERT: C 303 PHE cc_start: 0.7262 (m-80) cc_final: 0.6850 (m-80) REVERT: C 309 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7162 (mp0) REVERT: C 342 MET cc_start: 0.4810 (OUTLIER) cc_final: 0.4007 (mmm) REVERT: C 433 ARG cc_start: 0.7462 (tpt-90) cc_final: 0.7052 (mmm160) REVERT: C 459 ASN cc_start: 0.8477 (m-40) cc_final: 0.8151 (m110) REVERT: C 461 ARG cc_start: 0.7193 (mtp180) cc_final: 0.6841 (mtp85) REVERT: D 20 GLU cc_start: 0.7944 (mp0) cc_final: 0.7363 (mp0) REVERT: D 27 GLN cc_start: 0.8392 (mm110) cc_final: 0.8149 (mm-40) REVERT: D 28 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 32 GLN cc_start: 0.8171 (tp40) cc_final: 0.7918 (tp40) REVERT: D 42 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: D 78 TYR cc_start: 0.8646 (t80) cc_final: 0.8311 (t80) REVERT: D 81 ASP cc_start: 0.8496 (p0) cc_final: 0.8207 (p0) REVERT: D 109 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7627 (mt-10) REVERT: D 154 TYR cc_start: 0.8584 (t80) cc_final: 0.8246 (t80) REVERT: D 173 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8117 (mtp180) REVERT: D 179 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7488 (p) REVERT: D 182 GLU cc_start: 0.7493 (tt0) cc_final: 0.6791 (tm-30) REVERT: D 186 GLU cc_start: 0.8146 (tt0) cc_final: 0.7913 (tt0) REVERT: D 219 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7479 (tt0) REVERT: D 329 MET cc_start: 0.8100 (tpp) cc_final: 0.7750 (tpp) REVERT: D 348 PHE cc_start: 0.8032 (t80) cc_final: 0.7572 (t80) REVERT: D 351 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: D 409 ARG cc_start: 0.8794 (mmm160) cc_final: 0.8409 (mmm160) outliers start: 61 outliers final: 42 residues processed: 438 average time/residue: 0.1630 time to fit residues: 102.4796 Evaluate side-chains 465 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 410 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 249 THR 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 11 ARG Chi-restraints excluded: chain B residue 43 ASP 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 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 329 MET 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 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 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 201 VAL 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 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 42 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 127 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 226 GLN B 199 HIS B 274 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.178529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126029 restraints weight = 47545.349| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.06 r_work: 0.3274 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 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 = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20314 Z= 0.198 Angle : 0.620 8.637 28386 Z= 0.348 Chirality : 0.042 0.221 3109 Planarity : 0.005 0.042 3022 Dihedral : 23.220 87.894 4293 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % Rotamer: Outliers : 3.86 % Allowed : 18.82 % 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: 1.73 (0.19), residues: 1937 helix: 2.23 (0.17), residues: 912 sheet: -0.23 (0.29), residues: 296 loop : 0.49 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 2 TYR 0.021 0.002 TYR C 396 PHE 0.041 0.002 PHE C 314 TRP 0.020 0.001 TRP D 96 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (20298) covalent geometry : angle 0.61285 / 0.35 (28362) hydrogen bonds : bond 0.04481 / 3.10 ( 1060) hydrogen bonds : angle 3.73862 / 2.67 ( 2790) metal coordination : bond 0.00617 / 0.36 ( 16) metal coordination : angle 3.33900 / 2.00 ( 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 478 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 416 time to evaluate : 0.767 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 27 GLN cc_start: 0.7894 (mt0) cc_final: 0.7590 (mt0) REVERT: A 28 GLN cc_start: 0.8547 (tt0) cc_final: 0.8245 (tt0) REVERT: A 82 ARG cc_start: 0.8074 (mmt180) cc_final: 0.7390 (mmp80) REVERT: A 84 THR cc_start: 0.8117 (m) cc_final: 0.7899 (m) REVERT: A 98 GLU cc_start: 0.7370 (tp30) cc_final: 0.6871 (tp30) REVERT: A 100 HIS cc_start: 0.7999 (m170) cc_final: 0.7653 (m170) REVERT: A 113 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.7036 (t70) REVERT: A 137 ILE cc_start: 0.8572 (mt) cc_final: 0.8303 (tt) REVERT: A 147 PHE cc_start: 0.8684 (t80) cc_final: 0.8456 (t80) REVERT: A 155 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7491 (ptt90) REVERT: A 182 GLU cc_start: 0.7434 (tt0) cc_final: 0.7164 (tt0) REVERT: A 196 GLU cc_start: 0.8287 (pt0) cc_final: 0.8069 (pt0) REVERT: A 200 LEU cc_start: 0.8209 (mt) cc_final: 0.7936 (mt) REVERT: A 203 HIS cc_start: 0.7755 (t-90) cc_final: 0.7287 (t-90) REVERT: A 342 MET cc_start: 0.5251 (ttp) cc_final: 0.4918 (ttp) REVERT: A 376 GLU cc_start: 0.8447 (tt0) cc_final: 0.8224 (tt0) REVERT: A 383 GLU cc_start: 0.8913 (tt0) cc_final: 0.8494 (tt0) REVERT: A 407 ASP cc_start: 0.8259 (m-30) cc_final: 0.8015 (m-30) REVERT: A 409 ARG cc_start: 0.8765 (ttp-170) cc_final: 0.8474 (ptm160) REVERT: A 455 LEU cc_start: 0.9018 (mt) cc_final: 0.8583 (mm) REVERT: A 458 MET cc_start: 0.8156 (mmm) cc_final: 0.7171 (tmm) REVERT: A 481 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: B 7 ILE cc_start: 0.8017 (mm) cc_final: 0.7579 (mm) REVERT: B 43 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6532 (m-30) REVERT: B 51 ASP cc_start: 0.8304 (t0) cc_final: 0.8012 (t0) REVERT: B 79 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7322 (mtm110) REVERT: B 133 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 135 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 141 ASN cc_start: 0.8575 (m-40) cc_final: 0.8212 (m-40) REVERT: B 143 SER cc_start: 0.8590 (t) cc_final: 0.8380 (m) REVERT: B 155 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8111 (ptt90) REVERT: B 273 GLU cc_start: 0.8302 (tt0) cc_final: 0.8014 (mm-30) REVERT: B 284 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8102 (mtmm) REVERT: B 342 MET cc_start: 0.5118 (ttp) cc_final: 0.4677 (ttp) REVERT: B 371 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 443 TRP cc_start: 0.7828 (t-100) cc_final: 0.7259 (t-100) REVERT: B 458 MET cc_start: 0.8250 (mmt) cc_final: 0.7787 (mmp) REVERT: C 10 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7106 (t) REVERT: C 21 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7673 (tpp80) REVERT: C 24 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 46 VAL cc_start: 0.8625 (t) cc_final: 0.8402 (p) REVERT: C 54 ASP cc_start: 0.8046 (t0) cc_final: 0.7588 (t0) REVERT: C 69 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: C 92 GLN cc_start: 0.8315 (mt0) cc_final: 0.8056 (mt0) REVERT: C 135 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8104 (mm-30) REVERT: C 142 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7995 (ttp-110) REVERT: C 147 PHE cc_start: 0.8774 (t80) cc_final: 0.8432 (t80) REVERT: C 177 ASP cc_start: 0.7493 (t0) cc_final: 0.7160 (t0) REVERT: C 186 GLU cc_start: 0.8080 (tp30) cc_final: 0.7732 (tm-30) REVERT: C 187 VAL cc_start: 0.8256 (t) cc_final: 0.8018 (p) REVERT: C 199 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.6916 (p-80) REVERT: C 204 ASP cc_start: 0.8156 (t70) cc_final: 0.7443 (t70) REVERT: C 208 ARG cc_start: 0.8399 (mpp80) cc_final: 0.7846 (mpp80) REVERT: C 219 GLN cc_start: 0.8215 (tt0) cc_final: 0.8009 (tt0) REVERT: C 220 LEU cc_start: 0.8780 (tt) cc_final: 0.8387 (tt) REVERT: C 276 GLU cc_start: 0.7564 (tp30) cc_final: 0.7319 (tp30) REVERT: C 279 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7547 (mtt180) REVERT: C 281 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7903 (tp30) REVERT: C 300 ARG cc_start: 0.8274 (mmt180) cc_final: 0.8057 (mmt-90) REVERT: C 303 PHE cc_start: 0.7258 (m-80) cc_final: 0.6971 (m-80) REVERT: C 309 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7061 (mp0) REVERT: C 342 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.3988 (mmm) REVERT: C 404 GLU cc_start: 0.8311 (pt0) cc_final: 0.7981 (pp20) REVERT: C 433 ARG cc_start: 0.7542 (tpt-90) cc_final: 0.7100 (mmm160) REVERT: C 459 ASN cc_start: 0.8468 (m-40) cc_final: 0.8144 (m110) REVERT: C 461 ARG cc_start: 0.7002 (mtp180) cc_final: 0.6699 (mtp180) REVERT: D 20 GLU cc_start: 0.7717 (mp0) cc_final: 0.7171 (mp0) REVERT: D 22 GLN cc_start: 0.8172 (mt0) cc_final: 0.7945 (mt0) REVERT: D 28 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7364 (tm-30) REVERT: D 42 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: D 78 TYR cc_start: 0.8538 (t80) cc_final: 0.8177 (t80) REVERT: D 81 ASP cc_start: 0.8333 (p0) cc_final: 0.8035 (p0) REVERT: D 109 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7493 (mt-10) REVERT: D 118 PHE cc_start: 0.8404 (m-10) cc_final: 0.8121 (m-10) REVERT: D 154 TYR cc_start: 0.8552 (t80) cc_final: 0.8246 (t80) REVERT: D 179 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7387 (p) REVERT: D 182 GLU cc_start: 0.7241 (tt0) cc_final: 0.6651 (tm-30) REVERT: D 186 GLU cc_start: 0.7973 (tt0) cc_final: 0.7759 (tt0) REVERT: D 201 VAL cc_start: 0.8558 (t) cc_final: 0.8278 (p) REVERT: D 219 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7359 (tt0) REVERT: D 229 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7218 (pp20) REVERT: D 329 MET cc_start: 0.7974 (tpp) cc_final: 0.7629 (tpp) REVERT: D 351 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: D 409 ARG cc_start: 0.8739 (mmm160) cc_final: 0.8370 (mmm160) REVERT: D 464 PHE cc_start: 0.6389 (p90) cc_final: 0.6178 (p90) outliers start: 62 outliers final: 40 residues processed: 448 average time/residue: 0.1780 time to fit residues: 114.7764 Evaluate side-chains 466 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 411 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 249 THR 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 11 ARG Chi-restraints excluded: chain B residue 43 ASP 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 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER 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 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 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 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 199 HIS 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 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 42 GLU 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 200 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 133 optimal weight: 50.0000 chunk 22 optimal weight: 0.8980 chunk 202 optimal weight: 20.0000 chunk 186 optimal weight: 40.0000 chunk 126 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 226 GLN B 199 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.179812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128656 restraints weight = 37042.741| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.66 r_work: 0.3327 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20314 Z= 0.146 Angle : 0.602 9.227 28386 Z= 0.337 Chirality : 0.041 0.214 3109 Planarity : 0.005 0.044 3022 Dihedral : 23.194 88.145 4293 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % Rotamer: Outliers : 3.05 % Allowed : 19.44 % Favored : 77.51 % 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: 1.85 (0.20), residues: 1937 helix: 2.32 (0.17), residues: 912 sheet: -0.23 (0.30), residues: 286 loop : 0.56 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.018 0.002 TYR D 188 PHE 0.054 0.002 PHE D 348 TRP 0.041 0.001 TRP B 345 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (20298) covalent geometry : angle 0.59477 / 0.34 (28362) hydrogen bonds : bond 0.04113 / 2.86 ( 1060) hydrogen bonds : angle 3.70912 / 2.64 ( 2790) metal coordination : bond 0.00373 / 0.23 ( 16) metal coordination : angle 3.35742 / 2.09 ( 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 468 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 419 time to evaluate : 0.681 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 27 GLN cc_start: 0.7883 (mt0) cc_final: 0.7562 (mt0) REVERT: A 28 GLN cc_start: 0.8495 (tt0) cc_final: 0.8194 (tt0) REVERT: A 64 TRP cc_start: 0.8133 (m-10) cc_final: 0.7760 (m-10) REVERT: A 69 GLU cc_start: 0.6472 (mp0) cc_final: 0.5674 (mp0) REVERT: A 82 ARG cc_start: 0.8006 (mmt180) cc_final: 0.7208 (mmp80) REVERT: A 84 THR cc_start: 0.8059 (m) cc_final: 0.7859 (m) REVERT: A 98 GLU cc_start: 0.7309 (tp30) cc_final: 0.6806 (tp30) REVERT: A 100 HIS cc_start: 0.8008 (m170) cc_final: 0.7631 (m170) REVERT: A 137 ILE cc_start: 0.8552 (mt) cc_final: 0.8279 (tt) REVERT: A 147 PHE cc_start: 0.8663 (t80) cc_final: 0.8407 (t80) REVERT: A 155 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7425 (ptt90) REVERT: A 182 GLU cc_start: 0.7340 (tt0) cc_final: 0.7080 (tt0) REVERT: A 196 GLU cc_start: 0.8240 (pt0) cc_final: 0.7988 (pt0) REVERT: A 200 LEU cc_start: 0.8152 (mt) cc_final: 0.7881 (mt) REVERT: A 203 HIS cc_start: 0.7693 (t-90) cc_final: 0.7209 (t-90) REVERT: A 342 MET cc_start: 0.5120 (ttp) cc_final: 0.4791 (ttp) REVERT: A 376 GLU cc_start: 0.8412 (tt0) cc_final: 0.8172 (tt0) REVERT: A 383 GLU cc_start: 0.8878 (tt0) cc_final: 0.8436 (tt0) REVERT: A 407 ASP cc_start: 0.8169 (m-30) cc_final: 0.7923 (m-30) REVERT: A 409 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8367 (ptm160) REVERT: A 455 LEU cc_start: 0.9004 (mt) cc_final: 0.8672 (mp) REVERT: A 458 MET cc_start: 0.8061 (mmm) cc_final: 0.7104 (tmm) REVERT: A 481 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: B 51 ASP cc_start: 0.8287 (t0) cc_final: 0.8062 (t0) REVERT: B 79 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7191 (mtm110) REVERT: B 133 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7585 (mt-10) REVERT: B 135 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 141 ASN cc_start: 0.8555 (m-40) cc_final: 0.8317 (m-40) REVERT: B 155 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8071 (ptt180) REVERT: B 273 GLU cc_start: 0.8241 (tt0) cc_final: 0.7989 (tp30) REVERT: B 281 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 284 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8094 (mtmm) REVERT: B 342 MET cc_start: 0.4781 (ttp) cc_final: 0.4379 (ttp) REVERT: B 371 SER cc_start: 0.8477 (t) cc_final: 0.8227 (p) REVERT: B 379 GLU cc_start: 0.8464 (pt0) cc_final: 0.8041 (pp20) REVERT: B 416 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7731 (mmm-85) REVERT: B 458 MET cc_start: 0.8203 (mmt) cc_final: 0.7756 (mmp) REVERT: C 10 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.6743 (t) REVERT: C 21 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7552 (tpp80) REVERT: C 24 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 46 VAL cc_start: 0.8597 (t) cc_final: 0.8374 (p) REVERT: C 54 ASP cc_start: 0.8002 (t0) cc_final: 0.7576 (t0) REVERT: C 69 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: C 92 GLN cc_start: 0.8237 (mt0) cc_final: 0.7924 (mt0) REVERT: C 135 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 142 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7945 (ttp-110) REVERT: C 147 PHE cc_start: 0.8738 (t80) cc_final: 0.8400 (t80) REVERT: C 177 ASP cc_start: 0.7420 (t0) cc_final: 0.7105 (t0) REVERT: C 186 GLU cc_start: 0.8037 (tp30) cc_final: 0.7609 (tm-30) REVERT: C 187 VAL cc_start: 0.8226 (t) cc_final: 0.7885 (p) REVERT: C 199 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6865 (p-80) REVERT: C 204 ASP cc_start: 0.8124 (t70) cc_final: 0.7316 (t70) REVERT: C 208 ARG cc_start: 0.8347 (mpp80) cc_final: 0.7789 (mpp80) REVERT: C 219 GLN cc_start: 0.8135 (tt0) cc_final: 0.7923 (tt0) REVERT: C 228 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7845 (mtm-85) REVERT: C 240 ILE cc_start: 0.8247 (mm) cc_final: 0.7740 (tp) REVERT: C 276 GLU cc_start: 0.7492 (tp30) cc_final: 0.7242 (tp30) REVERT: C 279 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7325 (mtt180) REVERT: C 281 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7886 (tp30) REVERT: C 300 ARG cc_start: 0.8261 (mmt180) cc_final: 0.8048 (mmt-90) REVERT: C 303 PHE cc_start: 0.7219 (m-80) cc_final: 0.6982 (m-80) REVERT: C 309 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7035 (mp0) REVERT: C 342 MET cc_start: 0.4664 (OUTLIER) cc_final: 0.3951 (mmm) REVERT: C 404 GLU cc_start: 0.8259 (pt0) cc_final: 0.7928 (pp20) REVERT: C 433 ARG cc_start: 0.7480 (tpt-90) cc_final: 0.7044 (mmm160) REVERT: C 459 ASN cc_start: 0.8439 (m-40) cc_final: 0.8129 (m110) REVERT: C 461 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6667 (mtp180) REVERT: D 20 GLU cc_start: 0.7615 (mp0) cc_final: 0.7106 (mp0) REVERT: D 22 GLN cc_start: 0.8145 (mt0) cc_final: 0.7910 (mt0) REVERT: D 27 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7802 (mm-40) REVERT: D 28 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7314 (tm-30) REVERT: D 42 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: D 78 TYR cc_start: 0.8532 (t80) cc_final: 0.8166 (t80) REVERT: D 81 ASP cc_start: 0.8287 (p0) cc_final: 0.7986 (p0) REVERT: D 109 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7458 (mt-10) REVERT: D 118 PHE cc_start: 0.8375 (m-10) cc_final: 0.8063 (m-10) REVERT: D 154 TYR cc_start: 0.8490 (t80) cc_final: 0.8172 (t80) REVERT: D 182 GLU cc_start: 0.7112 (tt0) cc_final: 0.6552 (tm-30) REVERT: D 186 GLU cc_start: 0.7921 (tt0) cc_final: 0.7690 (tt0) REVERT: D 201 VAL cc_start: 0.8544 (t) cc_final: 0.8262 (p) REVERT: D 219 GLN cc_start: 0.7556 (tp-100) cc_final: 0.7271 (tt0) REVERT: D 229 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: D 329 MET cc_start: 0.7848 (tpp) cc_final: 0.7516 (tpp) REVERT: D 351 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: D 409 ARG cc_start: 0.8738 (mmm160) cc_final: 0.8349 (mmm160) outliers start: 49 outliers final: 30 residues processed: 447 average time/residue: 0.1801 time to fit residues: 115.4562 Evaluate side-chains 450 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 409 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 249 THR 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 11 ARG 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 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 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 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 199 HIS 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 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 42 GLU 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 205 LEU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 274 GLN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126702 restraints weight = 35962.199| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.62 r_work: 0.3303 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20314 Z= 0.233 Angle : 0.646 9.000 28386 Z= 0.360 Chirality : 0.043 0.236 3109 Planarity : 0.005 0.049 3022 Dihedral : 23.215 88.138 4291 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 2.99 % Allowed : 19.81 % Favored : 77.20 % 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: 1.65 (0.19), residues: 1937 helix: 2.16 (0.17), residues: 911 sheet: -0.32 (0.30), residues: 280 loop : 0.44 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 325 TYR 0.021 0.002 TYR D 324 PHE 0.038 0.002 PHE D 464 TRP 0.062 0.002 TRP B 345 HIS 0.013 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (20298) covalent geometry : angle 0.63918 / 0.36 (28362) hydrogen bonds : bond 0.04587 / 3.20 ( 1060) hydrogen bonds : angle 3.81210 / 2.72 ( 2790) metal coordination : bond 0.00714 / 0.44 ( 16) metal coordination : angle 3.27333 / 2.04 ( 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 457 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 409 time to evaluate : 0.747 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 27 GLN cc_start: 0.7911 (mt0) cc_final: 0.7593 (mt0) REVERT: A 28 GLN cc_start: 0.8545 (tt0) cc_final: 0.8247 (tt0) REVERT: A 69 GLU cc_start: 0.6434 (mp0) cc_final: 0.5954 (mp0) REVERT: A 82 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7361 (mmp80) REVERT: A 84 THR cc_start: 0.8168 (m) cc_final: 0.7946 (m) REVERT: A 98 GLU cc_start: 0.7334 (tp30) cc_final: 0.6835 (tp30) REVERT: A 100 HIS cc_start: 0.8024 (m170) cc_final: 0.7680 (m170) REVERT: A 137 ILE cc_start: 0.8550 (mt) cc_final: 0.8288 (tt) REVERT: A 147 PHE cc_start: 0.8656 (t80) cc_final: 0.8423 (t80) REVERT: A 155 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7421 (ptt90) REVERT: A 182 GLU cc_start: 0.7420 (tt0) cc_final: 0.7149 (tt0) REVERT: A 196 GLU cc_start: 0.8296 (pt0) cc_final: 0.7766 (pt0) REVERT: A 200 LEU cc_start: 0.8111 (mt) cc_final: 0.7850 (mt) REVERT: A 203 HIS cc_start: 0.7762 (t-90) cc_final: 0.7315 (t-90) REVERT: A 223 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7728 (mtm-85) REVERT: A 342 MET cc_start: 0.5233 (ttp) cc_final: 0.4904 (ttp) REVERT: A 376 GLU cc_start: 0.8423 (tt0) cc_final: 0.8192 (tt0) REVERT: A 383 GLU cc_start: 0.8905 (tt0) cc_final: 0.8490 (tt0) REVERT: A 407 ASP cc_start: 0.8210 (m-30) cc_final: 0.7922 (m-30) REVERT: A 409 ARG cc_start: 0.8755 (ttp-170) cc_final: 0.8466 (ptm160) REVERT: A 455 LEU cc_start: 0.9011 (mt) cc_final: 0.8669 (mp) REVERT: A 458 MET cc_start: 0.8183 (mmm) cc_final: 0.7179 (tmm) REVERT: A 481 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: B 79 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7290 (mtm180) REVERT: B 133 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 135 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 141 ASN cc_start: 0.8576 (m-40) cc_final: 0.8212 (m-40) REVERT: B 155 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8074 (ptt180) REVERT: B 273 GLU cc_start: 0.8239 (tt0) cc_final: 0.7851 (mm-30) REVERT: B 281 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7674 (tp30) REVERT: B 284 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8179 (mtmm) REVERT: B 342 MET cc_start: 0.4858 (ttp) cc_final: 0.4439 (ttp) REVERT: B 371 SER cc_start: 0.8523 (t) cc_final: 0.8316 (p) REVERT: B 379 GLU cc_start: 0.8469 (pt0) cc_final: 0.8046 (pp20) REVERT: B 443 TRP cc_start: 0.7747 (t-100) cc_final: 0.7191 (t-100) REVERT: B 458 MET cc_start: 0.8261 (mmt) cc_final: 0.7781 (mmp) REVERT: C 10 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7039 (t) REVERT: C 21 ARG cc_start: 0.7840 (mmm160) cc_final: 0.7566 (tpp80) REVERT: C 24 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 46 VAL cc_start: 0.8630 (t) cc_final: 0.8407 (p) REVERT: C 54 ASP cc_start: 0.8026 (t0) cc_final: 0.7604 (t0) REVERT: C 69 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: C 92 GLN cc_start: 0.8256 (mt0) cc_final: 0.7994 (mt0) REVERT: C 142 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7932 (ttp-110) REVERT: C 147 PHE cc_start: 0.8788 (t80) cc_final: 0.8514 (t80) REVERT: C 177 ASP cc_start: 0.7413 (t0) cc_final: 0.7111 (t0) REVERT: C 186 GLU cc_start: 0.8023 (tp30) cc_final: 0.7681 (tm-30) REVERT: C 187 VAL cc_start: 0.8243 (t) cc_final: 0.7940 (p) REVERT: C 199 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.6936 (p-80) REVERT: C 204 ASP cc_start: 0.8120 (t70) cc_final: 0.7341 (t70) REVERT: C 208 ARG cc_start: 0.8315 (mpp80) cc_final: 0.7754 (mpp80) REVERT: C 219 GLN cc_start: 0.8148 (tt0) cc_final: 0.7934 (tt0) REVERT: C 220 LEU cc_start: 0.8761 (tt) cc_final: 0.8366 (tt) REVERT: C 278 LEU cc_start: 0.8040 (mt) cc_final: 0.7767 (mm) REVERT: C 279 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7458 (mtt180) REVERT: C 281 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7815 (tp30) REVERT: C 300 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8075 (mmt-90) REVERT: C 303 PHE cc_start: 0.7300 (m-80) cc_final: 0.7049 (m-80) REVERT: C 309 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7091 (mp0) REVERT: C 342 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4113 (mmm) REVERT: C 433 ARG cc_start: 0.7527 (tpt-90) cc_final: 0.7109 (mmm160) REVERT: C 459 ASN cc_start: 0.8507 (m-40) cc_final: 0.8224 (m110) REVERT: C 461 ARG cc_start: 0.7004 (mtp180) cc_final: 0.6765 (mtp180) REVERT: D 20 GLU cc_start: 0.7644 (mp0) cc_final: 0.7135 (mp0) REVERT: D 22 GLN cc_start: 0.8168 (mt0) cc_final: 0.7955 (mt0) REVERT: D 27 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7893 (mm110) REVERT: D 28 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7349 (tm-30) REVERT: D 42 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: D 68 GLU cc_start: 0.8276 (tt0) cc_final: 0.7729 (tt0) REVERT: D 78 TYR cc_start: 0.8523 (t80) cc_final: 0.8143 (t80) REVERT: D 81 ASP cc_start: 0.8297 (p0) cc_final: 0.8002 (p0) REVERT: D 109 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7417 (mt-10) REVERT: D 118 PHE cc_start: 0.8394 (m-10) cc_final: 0.8107 (m-10) REVERT: D 154 TYR cc_start: 0.8538 (t80) cc_final: 0.8229 (t80) REVERT: D 182 GLU cc_start: 0.7201 (tt0) cc_final: 0.6626 (tm-30) REVERT: D 186 GLU cc_start: 0.7899 (tt0) cc_final: 0.7687 (tt0) REVERT: D 201 VAL cc_start: 0.8569 (t) cc_final: 0.8285 (p) REVERT: D 219 GLN cc_start: 0.7624 (tp-100) cc_final: 0.7314 (tt0) REVERT: D 229 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: D 329 MET cc_start: 0.7918 (tpp) cc_final: 0.7579 (tpp) REVERT: D 351 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: D 409 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8359 (mmm160) outliers start: 48 outliers final: 32 residues processed: 435 average time/residue: 0.1833 time to fit residues: 114.2686 Evaluate side-chains 451 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 408 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 11 ARG 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 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 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 474 ILE 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 76 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 199 HIS 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 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 42 GLU 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 205 LEU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 106 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 91 GLN B 199 HIS B 274 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.180207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129451 restraints weight = 34916.342| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.58 r_work: 0.3337 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20314 Z= 0.140 Angle : 0.605 8.955 28386 Z= 0.338 Chirality : 0.041 0.217 3109 Planarity : 0.005 0.043 3022 Dihedral : 23.191 88.367 4290 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.87 % Allowed : 19.94 % Favored : 77.20 % 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: 1.81 (0.20), residues: 1937 helix: 2.32 (0.17), residues: 912 sheet: -0.40 (0.29), residues: 285 loop : 0.57 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 325 TYR 0.021 0.002 TYR D 324 PHE 0.040 0.002 PHE C 348 TRP 0.046 0.001 TRP B 345 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (20298) covalent geometry : angle 0.59743 / 0.34 (28362) hydrogen bonds : bond 0.04063 / 2.83 ( 1060) hydrogen bonds : angle 3.71499 / 2.64 ( 2790) metal coordination : bond 0.00336 / 0.23 ( 16) metal coordination : angle 3.23901 / 1.97 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6953.02 seconds wall clock time: 118 minutes 51.97 seconds (7131.97 seconds total)