Starting phenix.real_space_refine on Fri Aug 7 06:47:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu2_60887/08_2026/9iu2_60887.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu2_60887/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu2_60887/08_2026/9iu2_60887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu2_60887/08_2026/9iu2_60887.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu2_60887/08_2026/9iu2_60887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu2_60887/08_2026/9iu2_60887.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 196 5.49 5 S 60 5.16 5 C 11581 2.51 5 N 3618 2.21 5 O 4023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.98, per 1000 atoms: 0.20 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: 1.20 Conformation dependent library (CDL) restraints added in 734.3 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: 1.83 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: 3.45 Time building geometry restraints manager: 1.66 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: 27053 4.30 - 8.59: 1248 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 1.90e+00 2.77e-01 1.28e+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 angle pdb=" O5' DT F 33 " pdb=" C5' DT F 33 " pdb=" C4' DT F 33 " ideal model delta sigma weight residual 109.40 117.35 -7.95 8.00e-01 1.56e+00 9.87e+01 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 1.90e+00 2.77e-01 8.64e+01 ... (remaining 28357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9422 17.92 - 35.84: 1272 35.84 - 53.77: 718 53.77 - 71.69: 184 71.69 - 89.61: 27 Dihedral angle restraints: 11623 sinusoidal: 6007 harmonic: 5616 Sorted by residual: dihedral pdb=" CA THR B 17 " pdb=" C THR B 17 " pdb=" N SER B 18 " pdb=" CA SER B 18 " ideal model delta harmonic sigma weight residual 180.00 143.77 36.23 0 5.00e+00 4.00e-02 5.25e+01 dihedral pdb=" CA LEU D 282 " pdb=" C LEU D 282 " pdb=" N VAL D 283 " pdb=" CA VAL D 283 " ideal model delta harmonic sigma weight residual -180.00 -148.13 -31.87 0 5.00e+00 4.00e-02 4.06e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N ALA A 15 " pdb=" CA ALA A 15 " ideal model delta harmonic sigma weight residual -180.00 -148.31 -31.69 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 11620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 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: 0.940 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: 0.070 Set scattering table: 0.050 Process input model: 19.630 Find NCS groups from input model: 0.330 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- 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= 0.779 Angle : 2.002 21.484 28386 Z= 1.346 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 1.98228 / 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 : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7347 (mmm) cc_final: 0.7106 (mmm) REVERT: A 24 GLU cc_start: 0.8926 (tt0) cc_final: 0.8622 (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: 0.7249 (tt) REVERT: A 140 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7454 (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: 0.7707 (p0) REVERT: B 85 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7450 (mtt90) REVERT: B 133 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6996 (mt-10) REVERT: B 135 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 139 GLU cc_start: 0.7901 (tt0) cc_final: 0.7611 (tt0) REVERT: B 141 ASN cc_start: 0.8060 (m-40) cc_final: 0.7744 (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: 0.7636 (ptt-90) REVERT: B 204 ASP cc_start: 0.7331 (t70) cc_final: 0.6977 (t0) REVERT: B 215 ASP cc_start: 0.7267 (m-30) cc_final: 0.7035 (m-30) REVERT: B 228 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6893 (mtt90) REVERT: B 242 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 257 ASP cc_start: 0.7098 (t70) cc_final: 0.6716 (t70) REVERT: B 267 GLU cc_start: 0.6649 (tt0) cc_final: 0.6386 (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: 0.3661 (ttp) REVERT: B 348 PHE cc_start: 0.8547 (t80) cc_final: 0.8326 (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: 0.7166 (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: 0.6983 (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: 0.7169 (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: 0.6547 (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: 0.8194 (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: 0.1591 time to fit residues: 121.5455 Evaluate side-chains 463 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 432 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 0.7980 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: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 199 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 452 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.182517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130675 restraints weight = 38121.014| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.70 r_work: 0.3357 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20314 Z= 0.181 Angle : 0.713 13.161 28386 Z= 0.396 Chirality : 0.050 0.318 3109 Planarity : 0.006 0.052 3022 Dihedral : 22.913 88.790 4343 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.93 % Allowed : 12.34 % Favored : 83.74 % 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: 1.91 (0.19), residues: 1937 helix: 2.26 (0.16), residues: 916 sheet: -0.10 (0.27), residues: 292 loop : 0.71 (0.24), residues: 729 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 0.017 0.002 PHE B 476 TRP 0.015 0.002 TRP A 64 HIS 0.009 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (20298) covalent geometry : angle 0.69880 / 0.40 (28362) hydrogen bonds : bond 0.05247 / 3.64 ( 1060) hydrogen bonds : angle 3.89440 / 2.80 ( 2790) metal coordination : bond 0.00754 / 0.42 ( 16) metal coordination : angle 4.99411 / 3.15 ( 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 474 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 411 time to evaluate : 0.545 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: 0.6282 (mmm) cc_final: 0.6073 (mmm) REVERT: A 28 GLN cc_start: 0.8538 (tt0) cc_final: 0.8297 (tt0) REVERT: A 33 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7406 (mmt90) REVERT: A 69 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6350 (mp0) REVERT: A 73 ASP cc_start: 0.6416 (m-30) cc_final: 0.6194 (m-30) REVERT: A 82 ARG cc_start: 0.7875 (mmt180) cc_final: 0.7227 (mmp80) REVERT: A 84 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7405 (m) REVERT: A 86 SER cc_start: 0.8236 (t) cc_final: 0.6977 (p) REVERT: A 98 GLU cc_start: 0.7235 (tp30) cc_final: 0.6878 (tp30) REVERT: A 100 HIS cc_start: 0.7953 (m170) cc_final: 0.7613 (m170) REVERT: A 137 ILE cc_start: 0.8686 (mt) cc_final: 0.8336 (tt) REVERT: A 147 PHE cc_start: 0.8669 (t80) cc_final: 0.8424 (t80) REVERT: A 205 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 376 GLU cc_start: 0.8434 (tt0) cc_final: 0.8154 (tt0) REVERT: A 409 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8470 (ptm160) REVERT: A 455 LEU cc_start: 0.8899 (mt) cc_final: 0.8547 (mm) REVERT: A 458 MET cc_start: 0.7764 (mmm) cc_final: 0.6921 (tmm) REVERT: A 481 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: B 1 MET cc_start: 0.7123 (mmm) cc_final: 0.6841 (mmm) REVERT: B 24 GLU cc_start: 0.7428 (tt0) cc_final: 0.7059 (tt0) REVERT: B 79 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7329 (mtm110) REVERT: B 85 ARG cc_start: 0.8263 (mtt90) cc_final: 0.8045 (mtt90) REVERT: B 133 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 135 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7848 (mm-30) REVERT: B 141 ASN cc_start: 0.8668 (m-40) cc_final: 0.8316 (m-40) REVERT: B 143 SER cc_start: 0.8737 (t) cc_final: 0.8509 (m) REVERT: B 153 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8409 (mttm) REVERT: B 155 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7915 (ptm160) REVERT: B 189 HIS cc_start: 0.8264 (m170) cc_final: 0.7824 (m-70) REVERT: B 204 ASP cc_start: 0.7943 (t70) cc_final: 0.7708 (t0) REVERT: B 273 GLU cc_start: 0.8263 (tt0) cc_final: 0.7943 (mm-30) REVERT: B 342 MET cc_start: 0.5060 (ttp) cc_final: 0.4551 (ttp) REVERT: B 348 PHE cc_start: 0.8436 (t80) cc_final: 0.8135 (t80) REVERT: B 441 ASP cc_start: 0.7646 (p0) cc_final: 0.7095 (p0) REVERT: B 458 MET cc_start: 0.8349 (mmt) cc_final: 0.8047 (mmm) REVERT: C 10 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.6610 (t) REVERT: C 21 ARG cc_start: 0.7683 (mmm160) cc_final: 0.7386 (tpp80) REVERT: C 24 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 46 VAL cc_start: 0.8415 (t) cc_final: 0.8146 (p) REVERT: C 54 ASP cc_start: 0.7791 (t0) cc_final: 0.7315 (t0) REVERT: C 57 ARG cc_start: 0.7307 (mmt90) cc_final: 0.6995 (mmt90) REVERT: C 69 GLU cc_start: 0.8275 (mp0) cc_final: 0.7680 (mm-30) REVERT: C 88 ARG cc_start: 0.7873 (mmm160) cc_final: 0.7342 (mmm160) REVERT: C 92 GLN cc_start: 0.7994 (mt0) cc_final: 0.7631 (mm-40) REVERT: C 118 PHE cc_start: 0.7693 (p90) cc_final: 0.7441 (p90) REVERT: C 147 PHE cc_start: 0.8627 (t80) cc_final: 0.8387 (t80) REVERT: C 163 TYR cc_start: 0.8370 (m-80) cc_final: 0.8111 (m-80) REVERT: C 186 GLU cc_start: 0.8128 (tp30) cc_final: 0.7633 (tm-30) REVERT: C 199 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6796 (p-80) REVERT: C 208 ARG cc_start: 0.8645 (mpp80) cc_final: 0.8359 (mtm-85) REVERT: C 220 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8551 (tp) REVERT: C 244 MET cc_start: 0.8080 (mmt) cc_final: 0.7832 (mmt) REVERT: C 267 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 279 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7317 (mtt180) REVERT: C 325 ARG cc_start: 0.6463 (ttp-170) cc_final: 0.5974 (tmm-80) REVERT: C 345 TRP cc_start: 0.7706 (m100) cc_final: 0.7356 (m100) REVERT: D 24 GLU cc_start: 0.7725 (tt0) cc_final: 0.7346 (tt0) REVERT: D 27 GLN cc_start: 0.8067 (mt0) cc_final: 0.7799 (mm110) REVERT: D 28 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 69 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 78 TYR cc_start: 0.8531 (t80) cc_final: 0.8234 (t80) REVERT: D 99 ASP cc_start: 0.7842 (m-30) cc_final: 0.7638 (m-30) REVERT: D 154 TYR cc_start: 0.8524 (t80) cc_final: 0.8150 (t80) REVERT: D 182 GLU cc_start: 0.7077 (tt0) cc_final: 0.6600 (tm-30) REVERT: D 185 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7965 (mm) REVERT: D 186 GLU cc_start: 0.7948 (tt0) cc_final: 0.7723 (tt0) REVERT: D 211 LEU cc_start: 0.8126 (mp) cc_final: 0.7770 (mt) REVERT: D 219 GLN cc_start: 0.7589 (tp-100) cc_final: 0.7234 (tt0) REVERT: D 242 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7867 (mt-10) REVERT: D 247 TYR cc_start: 0.8468 (m-10) cc_final: 0.8242 (m-10) REVERT: D 265 ARG cc_start: 0.8079 (ptt180) cc_final: 0.7831 (ptt180) REVERT: D 302 LEU cc_start: 0.8180 (tp) cc_final: 0.7905 (tp) REVERT: D 309 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6935 (mm-30) REVERT: D 329 MET cc_start: 0.7666 (tpp) cc_final: 0.7379 (tpp) REVERT: D 351 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: D 459 ASN cc_start: 0.8452 (m-40) cc_final: 0.8178 (m-40) REVERT: D 461 ARG cc_start: 0.6923 (ttm-80) cc_final: 0.6715 (ttm-80) REVERT: D 464 PHE cc_start: 0.6376 (p90) cc_final: 0.5727 (p90) outliers start: 63 outliers final: 29 residues processed: 448 average time/residue: 0.1657 time to fit residues: 107.7925 Evaluate side-chains 434 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 395 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 195 HIS Chi-restraints excluded: chain A residue 205 LEU 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 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 296 SER 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 185 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 148 ASN A 189 HIS A 195 HIS B 100 HIS B 199 HIS B 274 GLN B 437 GLN D 22 GLN D 111 HIS D 146 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.177223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125798 restraints weight = 32824.948| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.45 r_work: 0.3286 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 20314 Z= 0.366 Angle : 0.770 10.740 28386 Z= 0.422 Chirality : 0.051 0.291 3109 Planarity : 0.006 0.071 3022 Dihedral : 23.091 84.238 4308 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.93 % Allowed : 14.45 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 1937 helix: 1.94 (0.16), residues: 911 sheet: -0.35 (0.28), residues: 285 loop : 0.46 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 167 TYR 0.027 0.003 TYR C 154 PHE 0.021 0.002 PHE D 112 TRP 0.025 0.002 TRP C 172 HIS 0.019 0.002 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.37 (20298) covalent geometry : angle 0.75885 / 0.42 (28362) hydrogen bonds : bond 0.05959 / 4.14 ( 1060) hydrogen bonds : angle 4.04573 / 2.91 ( 2790) metal coordination : bond 0.01389 / 0.80 ( 16) metal coordination : angle 4.53677 / 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 471 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 408 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6096 (mmm) cc_final: 0.5894 (mmm) REVERT: A 28 GLN cc_start: 0.8543 (tt0) cc_final: 0.8251 (tt0) REVERT: A 73 ASP cc_start: 0.6541 (m-30) cc_final: 0.6311 (m-30) REVERT: A 82 ARG cc_start: 0.8004 (mmt180) cc_final: 0.7438 (mmp80) REVERT: A 84 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7938 (m) REVERT: A 98 GLU cc_start: 0.7345 (tp30) cc_final: 0.6925 (tp30) REVERT: A 100 HIS cc_start: 0.8000 (m170) cc_final: 0.7645 (m170) REVERT: A 137 ILE cc_start: 0.8526 (mt) cc_final: 0.8221 (tt) REVERT: A 147 PHE cc_start: 0.8601 (t80) cc_final: 0.8367 (t80) REVERT: A 182 GLU cc_start: 0.7341 (tt0) cc_final: 0.7084 (tt0) REVERT: A 203 HIS cc_start: 0.7739 (t-90) cc_final: 0.7328 (t-90) REVERT: A 219 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7274 (mm-40) REVERT: A 220 LEU cc_start: 0.8378 (mt) cc_final: 0.8067 (mt) REVERT: A 281 GLU cc_start: 0.8342 (tp30) cc_final: 0.8128 (tp30) REVERT: A 376 GLU cc_start: 0.8441 (tt0) cc_final: 0.8218 (tt0) REVERT: A 383 GLU cc_start: 0.8953 (tt0) cc_final: 0.8445 (tt0) REVERT: A 391 ILE cc_start: 0.6584 (mt) cc_final: 0.6329 (mt) REVERT: A 409 ARG cc_start: 0.8742 (ttp-170) cc_final: 0.8434 (ptm160) REVERT: A 455 LEU cc_start: 0.8961 (mt) cc_final: 0.8358 (mm) REVERT: A 458 MET cc_start: 0.8101 (mmm) cc_final: 0.7677 (tmm) REVERT: A 481 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: B 1 MET cc_start: 0.7638 (mmm) cc_final: 0.7292 (mmm) REVERT: B 7 ILE cc_start: 0.8000 (mm) cc_final: 0.7708 (mm) REVERT: B 79 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7480 (mtm110) REVERT: B 133 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7655 (mt-10) REVERT: B 135 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 141 ASN cc_start: 0.8620 (m-40) cc_final: 0.8224 (m-40) REVERT: B 143 SER cc_start: 0.8621 (t) cc_final: 0.8396 (m) REVERT: B 155 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8108 (ptm-80) REVERT: B 189 HIS cc_start: 0.8280 (m170) cc_final: 0.7841 (m-70) REVERT: B 204 ASP cc_start: 0.8052 (t70) cc_final: 0.7844 (t0) REVERT: B 273 GLU cc_start: 0.8231 (tt0) cc_final: 0.8014 (tt0) REVERT: B 342 MET cc_start: 0.5304 (ttp) cc_final: 0.4815 (ttp) REVERT: B 348 PHE cc_start: 0.8538 (t80) cc_final: 0.8263 (t80) REVERT: B 376 GLU cc_start: 0.8081 (tt0) cc_final: 0.7859 (tt0) REVERT: B 458 MET cc_start: 0.8345 (mmt) cc_final: 0.8063 (mmm) REVERT: C 10 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.7537 (t) REVERT: C 21 ARG cc_start: 0.7962 (mmm160) cc_final: 0.7690 (tpp80) REVERT: C 24 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 46 VAL cc_start: 0.8631 (t) cc_final: 0.8392 (p) REVERT: C 54 ASP cc_start: 0.8130 (t0) cc_final: 0.7518 (t70) REVERT: C 56 LYS cc_start: 0.7902 (tppp) cc_final: 0.7617 (tppp) REVERT: C 68 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 69 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: C 70 GLN cc_start: 0.8650 (mp10) cc_final: 0.8407 (mp10) REVERT: C 79 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7610 (mtp85) REVERT: C 81 ASP cc_start: 0.7926 (p0) cc_final: 0.7665 (p0) REVERT: C 92 GLN cc_start: 0.8180 (mt0) cc_final: 0.7976 (mt0) REVERT: C 116 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (p) REVERT: C 118 PHE cc_start: 0.7842 (p90) cc_final: 0.7581 (p90) REVERT: C 147 PHE cc_start: 0.8719 (t80) cc_final: 0.8475 (t80) REVERT: C 163 TYR cc_start: 0.8729 (m-80) cc_final: 0.8439 (m-80) REVERT: C 177 ASP cc_start: 0.7281 (t0) cc_final: 0.7062 (t0) REVERT: C 186 GLU cc_start: 0.8125 (tp30) cc_final: 0.7587 (tm-30) REVERT: C 199 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6837 (p-80) REVERT: C 208 ARG cc_start: 0.8590 (mpp80) cc_final: 0.8296 (mtm-85) REVERT: C 220 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8485 (tp) REVERT: C 242 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7479 (mt-10) REVERT: C 279 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7390 (mtt180) REVERT: C 309 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6803 (mp0) REVERT: C 342 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4125 (mmm) REVERT: C 433 ARG cc_start: 0.7364 (tpt-90) cc_final: 0.7161 (mmm160) REVERT: D 27 GLN cc_start: 0.8081 (mt0) cc_final: 0.7778 (mm110) REVERT: D 28 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7272 (tm-30) REVERT: D 32 GLN cc_start: 0.7854 (tp40) cc_final: 0.7646 (tp40) REVERT: D 78 TYR cc_start: 0.8528 (t80) cc_final: 0.8177 (t80) REVERT: D 109 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7386 (mt-10) REVERT: D 182 GLU cc_start: 0.7302 (tt0) cc_final: 0.6792 (tm-30) REVERT: D 185 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7989 (mm) REVERT: D 186 GLU cc_start: 0.7891 (tt0) cc_final: 0.7630 (tt0) REVERT: D 204 ASP cc_start: 0.7967 (t70) cc_final: 0.7614 (t0) REVERT: D 211 LEU cc_start: 0.8326 (mp) cc_final: 0.7947 (mt) REVERT: D 219 GLN cc_start: 0.7781 (tp-100) cc_final: 0.7414 (tt0) REVERT: D 224 GLU cc_start: 0.7546 (tp30) cc_final: 0.7261 (tp30) REVERT: D 265 ARG cc_start: 0.8381 (ptt180) cc_final: 0.8100 (ptt180) REVERT: D 309 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7227 (mm-30) REVERT: D 329 MET cc_start: 0.7875 (tpp) cc_final: 0.7588 (tpp) REVERT: D 348 PHE cc_start: 0.8072 (t80) cc_final: 0.7601 (t80) REVERT: D 351 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: D 464 PHE cc_start: 0.6407 (p90) cc_final: 0.5956 (p90) outliers start: 63 outliers final: 44 residues processed: 438 average time/residue: 0.1602 time to fit residues: 102.8935 Evaluate side-chains 459 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 404 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 133 GLU 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 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 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 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 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 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 7 ILE 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 185 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 GLU 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: 1.9990 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS A 226 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 274 GLN C 111 HIS C 480 GLN 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 = 0.4204 r_free = 0.4204 target = 0.179482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127073 restraints weight = 44223.600| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.93 r_work: 0.3290 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20314 Z= 0.185 Angle : 0.620 8.517 28386 Z= 0.348 Chirality : 0.043 0.218 3109 Planarity : 0.005 0.045 3022 Dihedral : 23.182 86.133 4304 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.17 % Allowed : 15.14 % Favored : 80.69 % 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: 1.84 (0.19), residues: 1937 helix: 2.27 (0.16), residues: 912 sheet: -0.18 (0.30), residues: 281 loop : 0.59 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 150 TYR 0.018 0.002 TYR D 188 PHE 0.020 0.002 PHE C 314 TRP 0.019 0.001 TRP D 96 HIS 0.011 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (20298) covalent geometry : angle 0.61017 / 0.35 (28362) hydrogen bonds : bond 0.04647 / 3.23 ( 1060) hydrogen bonds : angle 3.78034 / 2.71 ( 2790) metal coordination : bond 0.00641 / 0.37 ( 16) metal coordination : angle 3.73954 / 2.32 ( 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 474 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 407 time to evaluate : 0.638 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 28 GLN cc_start: 0.8584 (tt0) cc_final: 0.8261 (tt0) REVERT: A 69 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6539 (mp0) REVERT: A 82 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7471 (mmp80) REVERT: A 84 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7809 (m) REVERT: A 98 GLU cc_start: 0.7347 (tp30) cc_final: 0.6930 (tp30) REVERT: A 100 HIS cc_start: 0.8024 (m170) cc_final: 0.7683 (m170) REVERT: A 137 ILE cc_start: 0.8583 (mt) cc_final: 0.8291 (tt) REVERT: A 147 PHE cc_start: 0.8668 (t80) cc_final: 0.8408 (t80) REVERT: A 155 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7381 (ptm160) REVERT: A 182 GLU cc_start: 0.7281 (tt0) cc_final: 0.7024 (tt0) REVERT: A 200 LEU cc_start: 0.8225 (mt) cc_final: 0.7966 (mt) REVERT: A 203 HIS cc_start: 0.7741 (t-90) cc_final: 0.7271 (t-90) REVERT: A 220 LEU cc_start: 0.8369 (mt) cc_final: 0.8020 (mt) REVERT: A 376 GLU cc_start: 0.8466 (tt0) cc_final: 0.8243 (tt0) REVERT: A 383 GLU cc_start: 0.8943 (tt0) cc_final: 0.8456 (tt0) REVERT: A 391 ILE cc_start: 0.6670 (mt) cc_final: 0.6425 (mt) REVERT: A 409 ARG cc_start: 0.8724 (ttp-170) cc_final: 0.8432 (ptm160) REVERT: A 455 LEU cc_start: 0.8944 (mt) cc_final: 0.8337 (mm) REVERT: A 458 MET cc_start: 0.8063 (mmm) cc_final: 0.7601 (tmm) REVERT: A 481 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: B 1 MET cc_start: 0.7619 (mmm) cc_final: 0.7403 (mmm) REVERT: B 7 ILE cc_start: 0.7894 (mm) cc_final: 0.7694 (mm) REVERT: B 79 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7369 (mtm110) REVERT: B 133 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 135 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 141 ASN cc_start: 0.8629 (m-40) cc_final: 0.8253 (m-40) REVERT: B 143 SER cc_start: 0.8639 (t) cc_final: 0.8418 (m) REVERT: B 155 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8051 (ptm160) REVERT: B 189 HIS cc_start: 0.8305 (m170) cc_final: 0.7884 (m-70) REVERT: B 221 GLN cc_start: 0.7822 (mm110) cc_final: 0.7435 (mm110) REVERT: B 273 GLU cc_start: 0.8271 (tt0) cc_final: 0.8031 (tt0) REVERT: B 284 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8026 (mtmm) REVERT: B 342 MET cc_start: 0.5246 (ttp) cc_final: 0.4748 (ttp) REVERT: B 348 PHE cc_start: 0.8582 (t80) cc_final: 0.8285 (t80) REVERT: B 376 GLU cc_start: 0.8116 (tt0) cc_final: 0.7873 (tt0) REVERT: B 458 MET cc_start: 0.8356 (mmt) cc_final: 0.8071 (mmm) REVERT: C 10 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7147 (t) REVERT: C 21 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7649 (tpp80) REVERT: C 24 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 46 VAL cc_start: 0.8633 (t) cc_final: 0.8399 (p) REVERT: C 54 ASP cc_start: 0.8144 (t0) cc_final: 0.7718 (t0) REVERT: C 56 LYS cc_start: 0.7933 (tppp) cc_final: 0.7707 (tppp) REVERT: C 69 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: C 92 GLN cc_start: 0.8242 (mt0) cc_final: 0.8016 (mt0) REVERT: C 99 ASP cc_start: 0.7109 (m-30) cc_final: 0.6851 (m-30) REVERT: C 118 PHE cc_start: 0.7734 (p90) cc_final: 0.7434 (p90) REVERT: C 140 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7678 (mpp80) REVERT: C 142 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7995 (ttp-110) REVERT: C 147 PHE cc_start: 0.8738 (t80) cc_final: 0.8431 (t80) REVERT: C 163 TYR cc_start: 0.8731 (m-80) cc_final: 0.8392 (m-80) REVERT: C 186 GLU cc_start: 0.8126 (tp30) cc_final: 0.7774 (tp30) REVERT: C 199 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6754 (p-80) REVERT: C 203 HIS cc_start: 0.7930 (t70) cc_final: 0.7670 (t70) REVERT: C 208 ARG cc_start: 0.8606 (mpp80) cc_final: 0.8322 (mtm-85) REVERT: C 220 LEU cc_start: 0.8754 (tt) cc_final: 0.8442 (tt) REVERT: C 242 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 267 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7873 (mm-30) REVERT: C 279 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7428 (mtt180) REVERT: C 300 ARG cc_start: 0.8359 (mmt180) cc_final: 0.8115 (mmt180) REVERT: C 309 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6758 (mp0) REVERT: C 342 MET cc_start: 0.4743 (OUTLIER) cc_final: 0.3993 (mmm) REVERT: C 433 ARG cc_start: 0.7388 (tpt-90) cc_final: 0.7164 (mmm160) REVERT: C 461 ARG cc_start: 0.6871 (mtm110) cc_final: 0.6388 (ttt180) REVERT: C 480 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8183 (pp30) REVERT: D 27 GLN cc_start: 0.8159 (mt0) cc_final: 0.7900 (mm110) REVERT: D 28 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7311 (tm-30) REVERT: D 32 GLN cc_start: 0.7896 (tp40) cc_final: 0.7672 (tp40) REVERT: D 78 TYR cc_start: 0.8548 (t80) cc_final: 0.8238 (t80) REVERT: D 109 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7399 (mt-10) REVERT: D 154 TYR cc_start: 0.8509 (t80) cc_final: 0.8107 (t80) REVERT: D 155 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7870 (ptt90) REVERT: D 179 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7315 (p) REVERT: D 182 GLU cc_start: 0.7316 (tt0) cc_final: 0.6754 (tm-30) REVERT: D 185 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7957 (mm) REVERT: D 186 GLU cc_start: 0.7957 (tt0) cc_final: 0.7677 (tt0) REVERT: D 204 ASP cc_start: 0.8017 (t70) cc_final: 0.7647 (t0) REVERT: D 211 LEU cc_start: 0.8334 (mp) cc_final: 0.8011 (mt) REVERT: D 219 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7383 (tt0) REVERT: D 265 ARG cc_start: 0.8377 (ptt180) cc_final: 0.8124 (ptt180) REVERT: D 329 MET cc_start: 0.7885 (tpp) cc_final: 0.7573 (tpp) REVERT: D 348 PHE cc_start: 0.8020 (t80) cc_final: 0.7696 (t80) REVERT: D 351 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: D 464 PHE cc_start: 0.6417 (p90) cc_final: 0.6100 (p90) outliers start: 67 outliers final: 41 residues processed: 442 average time/residue: 0.1658 time to fit residues: 106.2515 Evaluate side-chains 453 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 397 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 155 ARG 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 11 ARG 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 286 SER Chi-restraints excluded: chain B residue 329 MET 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 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 140 ARG 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 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 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 185 LEU 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 396 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 103 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN B 199 HIS B 274 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 480 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 = 0.4219 r_free = 0.4219 target = 0.180640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129481 restraints weight = 34299.349| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.54 r_work: 0.3345 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- 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 = 0.47 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20314 Z= 0.141 Angle : 0.584 8.293 28386 Z= 0.330 Chirality : 0.041 0.227 3109 Planarity : 0.005 0.049 3022 Dihedral : 23.124 87.532 4298 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.93 % Allowed : 15.08 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 1937 helix: 2.42 (0.16), residues: 912 sheet: -0.14 (0.30), residues: 282 loop : 0.70 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 409 TYR 0.016 0.001 TYR D 188 PHE 0.027 0.001 PHE C 314 TRP 0.021 0.001 TRP A 64 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (20298) covalent geometry : angle 0.57622 / 0.33 (28362) hydrogen bonds : bond 0.04295 / 2.98 ( 1060) hydrogen bonds : angle 3.70466 / 2.64 ( 2790) metal coordination : bond 0.00439 / 0.27 ( 16) metal coordination : angle 3.37044 / 2.08 ( 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 460 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 397 time to evaluate : 0.525 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 28 GLN cc_start: 0.8512 (tt0) cc_final: 0.8237 (tt0) REVERT: A 82 ARG cc_start: 0.8041 (mmt180) cc_final: 0.7346 (mmp80) REVERT: A 84 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7805 (m) REVERT: A 98 GLU cc_start: 0.7290 (tp30) cc_final: 0.6825 (tp30) REVERT: A 100 HIS cc_start: 0.7996 (m170) cc_final: 0.7648 (m170) REVERT: A 137 ILE cc_start: 0.8564 (mt) cc_final: 0.8294 (tt) REVERT: A 147 PHE cc_start: 0.8636 (t80) cc_final: 0.8358 (t80) REVERT: A 155 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7113 (ptt90) REVERT: A 203 HIS cc_start: 0.7638 (t-90) cc_final: 0.7161 (t-90) REVERT: A 220 LEU cc_start: 0.8334 (mt) cc_final: 0.7970 (tt) REVERT: A 376 GLU cc_start: 0.8402 (tt0) cc_final: 0.8169 (tt0) REVERT: A 383 GLU cc_start: 0.8878 (tt0) cc_final: 0.8414 (tt0) REVERT: A 391 ILE cc_start: 0.6543 (mt) cc_final: 0.6300 (mt) REVERT: A 409 ARG cc_start: 0.8684 (ttp-170) cc_final: 0.8369 (ptm160) REVERT: A 455 LEU cc_start: 0.8948 (mt) cc_final: 0.8337 (mm) REVERT: A 458 MET cc_start: 0.8032 (mmm) cc_final: 0.7605 (tmm) REVERT: A 481 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: B 68 GLU cc_start: 0.6811 (pt0) cc_final: 0.6432 (pp20) REVERT: B 79 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7243 (mtm180) REVERT: B 133 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7591 (mt-10) REVERT: B 135 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 141 ASN cc_start: 0.8591 (m-40) cc_final: 0.8226 (m-40) REVERT: B 143 SER cc_start: 0.8613 (t) cc_final: 0.8392 (m) REVERT: B 155 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7870 (ptm160) REVERT: B 189 HIS cc_start: 0.8233 (m170) cc_final: 0.7928 (m-70) REVERT: B 221 GLN cc_start: 0.7752 (mm110) cc_final: 0.7351 (mm110) REVERT: B 284 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8005 (mtmm) REVERT: B 342 MET cc_start: 0.5153 (ttp) cc_final: 0.4649 (ttp) REVERT: B 348 PHE cc_start: 0.8622 (t80) cc_final: 0.8335 (t80) REVERT: B 371 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8042 (p) REVERT: B 376 GLU cc_start: 0.8050 (tt0) cc_final: 0.7779 (tt0) REVERT: B 458 MET cc_start: 0.8307 (mmt) cc_final: 0.8005 (mmm) REVERT: C 10 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.6689 (t) REVERT: C 21 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7482 (tpp80) REVERT: C 24 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7516 (tm-30) REVERT: C 46 VAL cc_start: 0.8604 (t) cc_final: 0.8391 (p) REVERT: C 54 ASP cc_start: 0.8112 (t0) cc_final: 0.7749 (t0) REVERT: C 56 LYS cc_start: 0.7887 (tppp) cc_final: 0.7656 (tppp) REVERT: C 69 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: C 79 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7473 (mtp85) REVERT: C 92 GLN cc_start: 0.8204 (mt0) cc_final: 0.7969 (mt0) REVERT: C 99 ASP cc_start: 0.7011 (m-30) cc_final: 0.6800 (m-30) REVERT: C 142 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7953 (ttp-110) REVERT: C 147 PHE cc_start: 0.8719 (t80) cc_final: 0.8390 (t80) REVERT: C 163 TYR cc_start: 0.8693 (m-80) cc_final: 0.8321 (m-80) REVERT: C 186 GLU cc_start: 0.8066 (tp30) cc_final: 0.7556 (tm-30) REVERT: C 199 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6734 (p-80) REVERT: C 203 HIS cc_start: 0.7831 (t70) cc_final: 0.7596 (t70) REVERT: C 208 ARG cc_start: 0.8546 (mpp80) cc_final: 0.8142 (mtm-85) REVERT: C 220 LEU cc_start: 0.8708 (tt) cc_final: 0.8316 (tt) REVERT: C 242 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 267 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7831 (mm-30) REVERT: C 300 ARG cc_start: 0.8381 (mmt180) cc_final: 0.7934 (mmt-90) REVERT: C 303 PHE cc_start: 0.7139 (m-80) cc_final: 0.6592 (m-80) REVERT: C 309 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6780 (mp0) REVERT: C 325 ARG cc_start: 0.6604 (tmm-80) cc_final: 0.6260 (ttp80) REVERT: C 342 MET cc_start: 0.4638 (OUTLIER) cc_final: 0.3905 (mmm) REVERT: C 352 GLN cc_start: 0.7804 (tt0) cc_final: 0.7461 (pt0) REVERT: C 433 ARG cc_start: 0.7330 (tpt-90) cc_final: 0.7099 (mmm160) REVERT: C 461 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6261 (tpp-160) REVERT: D 27 GLN cc_start: 0.8122 (mt0) cc_final: 0.7905 (mm110) REVERT: D 28 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7281 (tm-30) REVERT: D 32 GLN cc_start: 0.7840 (tp40) cc_final: 0.7616 (tp40) REVERT: D 42 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: D 78 TYR cc_start: 0.8515 (t80) cc_final: 0.8188 (t80) REVERT: D 109 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7384 (mt-10) REVERT: D 154 TYR cc_start: 0.8477 (t80) cc_final: 0.8075 (t80) REVERT: D 179 VAL cc_start: 0.7441 (OUTLIER) cc_final: 0.7200 (p) REVERT: D 182 GLU cc_start: 0.7119 (tt0) cc_final: 0.6608 (tm-30) REVERT: D 185 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7931 (mm) REVERT: D 186 GLU cc_start: 0.7877 (tt0) cc_final: 0.7641 (tt0) REVERT: D 204 ASP cc_start: 0.7970 (t70) cc_final: 0.7567 (t0) REVERT: D 211 LEU cc_start: 0.8304 (mp) cc_final: 0.7991 (mt) REVERT: D 219 GLN cc_start: 0.7640 (tp-100) cc_final: 0.7319 (tt0) REVERT: D 247 TYR cc_start: 0.8509 (m-10) cc_final: 0.8298 (m-10) REVERT: D 265 ARG cc_start: 0.8319 (ptt180) cc_final: 0.8080 (ptt180) REVERT: D 309 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7282 (mm-30) REVERT: D 329 MET cc_start: 0.7802 (tpp) cc_final: 0.7514 (tpp) REVERT: D 351 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: D 464 PHE cc_start: 0.6343 (p90) cc_final: 0.6047 (p90) outliers start: 63 outliers final: 41 residues processed: 433 average time/residue: 0.1668 time to fit residues: 104.4944 Evaluate side-chains 445 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 389 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 SER 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 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 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 480 GLN 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 185 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 219 GLN A 334 HIS B 148 ASN B 199 HIS ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 480 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 = 0.4173 r_free = 0.4173 target = 0.176901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125345 restraints weight = 36702.378| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.61 r_work: 0.3273 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 20314 Z= 0.347 Angle : 0.713 10.042 28386 Z= 0.393 Chirality : 0.048 0.269 3109 Planarity : 0.006 0.048 3022 Dihedral : 23.271 87.073 4298 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.49 % Allowed : 15.95 % Favored : 79.56 % 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: 1.49 (0.19), residues: 1937 helix: 1.96 (0.16), residues: 913 sheet: -0.30 (0.29), residues: 295 loop : 0.44 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 2 TYR 0.026 0.003 TYR B 163 PHE 0.036 0.002 PHE C 118 TRP 0.021 0.002 TRP A 64 HIS 0.012 0.002 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.35 (20298) covalent geometry : angle 0.70522 / 0.39 (28362) hydrogen bonds : bond 0.05472 / 3.80 ( 1060) hydrogen bonds : angle 3.94099 / 2.82 ( 2790) metal coordination : bond 0.01201 / 0.72 ( 16) metal coordination : angle 3.56554 / 2.10 ( 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 489 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 417 time to evaluate : 0.551 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: A 1 MET cc_start: 0.6222 (mmm) cc_final: 0.5796 (mmm) REVERT: A 28 GLN cc_start: 0.8492 (tt0) cc_final: 0.8213 (tt0) REVERT: A 64 TRP cc_start: 0.8270 (m-10) cc_final: 0.7946 (m-10) REVERT: A 82 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7476 (mmp80) REVERT: A 84 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7956 (m) REVERT: A 98 GLU cc_start: 0.7379 (tp30) cc_final: 0.6911 (tp30) REVERT: A 100 HIS cc_start: 0.7961 (m170) cc_final: 0.7599 (m170) REVERT: A 116 THR cc_start: 0.6594 (OUTLIER) cc_final: 0.5786 (p) REVERT: A 137 ILE cc_start: 0.8502 (mt) cc_final: 0.8241 (tt) REVERT: A 147 PHE cc_start: 0.8637 (t80) cc_final: 0.8411 (t80) REVERT: A 155 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7761 (ppt170) REVERT: A 164 LEU cc_start: 0.8298 (mm) cc_final: 0.8063 (mt) REVERT: A 182 GLU cc_start: 0.7452 (tt0) cc_final: 0.7185 (tt0) REVERT: A 200 LEU cc_start: 0.8267 (mt) cc_final: 0.8050 (mt) REVERT: A 203 HIS cc_start: 0.7746 (t-90) cc_final: 0.7300 (t-90) REVERT: A 220 LEU cc_start: 0.8401 (mt) cc_final: 0.8191 (tp) REVERT: A 281 GLU cc_start: 0.8329 (tp30) cc_final: 0.8092 (tp30) REVERT: A 376 GLU cc_start: 0.8444 (tt0) cc_final: 0.8233 (tt0) REVERT: A 383 GLU cc_start: 0.8898 (tt0) cc_final: 0.8465 (tt0) REVERT: A 391 ILE cc_start: 0.6748 (mt) cc_final: 0.6538 (mt) REVERT: A 407 ASP cc_start: 0.8139 (m-30) cc_final: 0.7921 (m-30) REVERT: A 409 ARG cc_start: 0.8729 (ttp-170) cc_final: 0.8440 (ptm160) REVERT: A 455 LEU cc_start: 0.8985 (mt) cc_final: 0.8379 (mm) REVERT: A 458 MET cc_start: 0.8199 (mmm) cc_final: 0.7521 (tmm) REVERT: A 481 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: B 79 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7411 (mtm180) REVERT: B 133 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7610 (mt-10) REVERT: B 135 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 141 ASN cc_start: 0.8592 (m-40) cc_final: 0.8195 (m-40) REVERT: B 155 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7993 (ptm160) REVERT: B 284 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8042 (mtmm) REVERT: B 342 MET cc_start: 0.5268 (ttp) cc_final: 0.4800 (ttp) REVERT: B 345 TRP cc_start: 0.6900 (m100) cc_final: 0.6694 (m100) REVERT: B 376 GLU cc_start: 0.8132 (tt0) cc_final: 0.7880 (tt0) REVERT: B 458 MET cc_start: 0.8236 (mmt) cc_final: 0.7798 (mmp) REVERT: C 10 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7468 (t) REVERT: C 21 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7659 (tpp80) REVERT: C 24 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 46 VAL cc_start: 0.8661 (t) cc_final: 0.8422 (p) REVERT: C 54 ASP cc_start: 0.8180 (t0) cc_final: 0.7865 (t0) REVERT: C 56 LYS cc_start: 0.7945 (tppp) cc_final: 0.7740 (tppp) REVERT: C 57 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7267 (mmt90) REVERT: C 69 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: C 79 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7554 (mtp85) REVERT: C 92 GLN cc_start: 0.8274 (mt0) cc_final: 0.8031 (mt0) REVERT: C 132 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7865 (mtp) REVERT: C 147 PHE cc_start: 0.8772 (t80) cc_final: 0.8476 (t80) REVERT: C 177 ASP cc_start: 0.7426 (t0) cc_final: 0.7135 (t0) REVERT: C 186 GLU cc_start: 0.8121 (tp30) cc_final: 0.7779 (tp30) REVERT: C 199 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.6882 (p-80) REVERT: C 208 ARG cc_start: 0.8590 (mpp80) cc_final: 0.8198 (mtm-85) REVERT: C 220 LEU cc_start: 0.8784 (tt) cc_final: 0.8529 (tp) REVERT: C 240 ILE cc_start: 0.8365 (mm) cc_final: 0.7871 (tt) REVERT: C 242 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7579 (mt-10) REVERT: C 279 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7543 (mtt180) REVERT: C 283 VAL cc_start: 0.7309 (t) cc_final: 0.7105 (p) REVERT: C 300 ARG cc_start: 0.8393 (mmt180) cc_final: 0.8148 (mmt-90) REVERT: C 309 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6930 (mp0) REVERT: C 342 MET cc_start: 0.4782 (OUTLIER) cc_final: 0.4024 (mmm) REVERT: C 352 GLN cc_start: 0.8005 (tt0) cc_final: 0.7693 (pt0) REVERT: C 433 ARG cc_start: 0.7480 (tpt-90) cc_final: 0.7192 (mmm160) REVERT: C 459 ASN cc_start: 0.8586 (m-40) cc_final: 0.8234 (m110) REVERT: C 480 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: D 20 GLU cc_start: 0.7634 (mp0) cc_final: 0.7108 (mp0) REVERT: D 27 GLN cc_start: 0.8178 (mt0) cc_final: 0.7946 (mm110) REVERT: D 28 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 32 GLN cc_start: 0.7911 (tp40) cc_final: 0.7663 (tp40) REVERT: D 42 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: D 78 TYR cc_start: 0.8509 (t80) cc_final: 0.8173 (t80) REVERT: D 81 ASP cc_start: 0.8291 (p0) cc_final: 0.7988 (p0) REVERT: D 109 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7423 (mt-10) REVERT: D 154 TYR cc_start: 0.8595 (t80) cc_final: 0.8306 (t80) REVERT: D 179 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7536 (p) REVERT: D 182 GLU cc_start: 0.7313 (tt0) cc_final: 0.6745 (tm-30) REVERT: D 186 GLU cc_start: 0.7939 (tt0) cc_final: 0.7719 (tt0) REVERT: D 204 ASP cc_start: 0.8045 (t70) cc_final: 0.7683 (t0) REVERT: D 211 LEU cc_start: 0.8367 (mp) cc_final: 0.8054 (mt) REVERT: D 219 GLN cc_start: 0.7695 (tp-100) cc_final: 0.7367 (tt0) REVERT: D 265 ARG cc_start: 0.8406 (ptt180) cc_final: 0.8125 (ptt180) REVERT: D 329 MET cc_start: 0.7973 (tpp) cc_final: 0.7693 (tpp) REVERT: D 351 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: D 409 ARG cc_start: 0.8756 (mmm160) cc_final: 0.8475 (mmm160) REVERT: D 464 PHE cc_start: 0.6410 (p90) cc_final: 0.6180 (p90) outliers start: 72 outliers final: 48 residues processed: 455 average time/residue: 0.1454 time to fit residues: 96.4872 Evaluate side-chains 466 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 404 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 84 THR 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 205 LEU 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 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 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 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 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 473 THR Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 7 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 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 Chi-restraints excluded: chain D residue 453 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 138 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 226 GLN B 148 ASN B 199 HIS B 352 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.179795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129271 restraints weight = 31572.135| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.42 r_work: 0.3340 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20314 Z= 0.150 Angle : 0.607 8.094 28386 Z= 0.339 Chirality : 0.042 0.220 3109 Planarity : 0.005 0.043 3022 Dihedral : 23.228 87.477 4296 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.68 % Allowed : 17.76 % Favored : 78.57 % 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 (0.19), residues: 1937 helix: 2.30 (0.17), residues: 912 sheet: -0.19 (0.29), residues: 292 loop : 0.52 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 173 TYR 0.019 0.002 TYR C 396 PHE 0.038 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 0.00284 / 0.15 (20298) covalent geometry : angle 0.59887 / 0.34 (28362) hydrogen bonds : bond 0.04332 / 3.01 ( 1060) hydrogen bonds : angle 3.74259 / 2.67 ( 2790) metal coordination : bond 0.00435 / 0.26 ( 16) metal coordination : angle 3.42239 / 2.06 ( 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 464 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 405 time to evaluate : 0.457 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: A 27 GLN cc_start: 0.7879 (mt0) cc_final: 0.7591 (mt0) REVERT: A 28 GLN cc_start: 0.8542 (tt0) cc_final: 0.8254 (tt0) REVERT: A 64 TRP cc_start: 0.8230 (m-90) cc_final: 0.7829 (m-10) REVERT: A 69 GLU cc_start: 0.6700 (mp0) cc_final: 0.6393 (mp0) REVERT: A 82 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7404 (mmp80) REVERT: A 84 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7878 (m) REVERT: A 98 GLU cc_start: 0.7481 (tp30) cc_final: 0.7045 (tp30) REVERT: A 100 HIS cc_start: 0.8097 (m170) cc_final: 0.7735 (m170) REVERT: A 137 ILE cc_start: 0.8673 (mt) cc_final: 0.8387 (tt) REVERT: A 147 PHE cc_start: 0.8782 (t80) cc_final: 0.8537 (t80) REVERT: A 155 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7436 (ptt90) REVERT: A 182 GLU cc_start: 0.7549 (tt0) cc_final: 0.7291 (tt0) REVERT: A 196 GLU cc_start: 0.8523 (pt0) cc_final: 0.8208 (pt0) REVERT: A 203 HIS cc_start: 0.7899 (t-90) cc_final: 0.7425 (t-90) REVERT: A 220 LEU cc_start: 0.8409 (mt) cc_final: 0.8083 (tt) REVERT: A 376 GLU cc_start: 0.8492 (tt0) cc_final: 0.8279 (tt0) REVERT: A 383 GLU cc_start: 0.8957 (tt0) cc_final: 0.8559 (tt0) REVERT: A 391 ILE cc_start: 0.6956 (mt) cc_final: 0.6734 (mt) REVERT: A 407 ASP cc_start: 0.8223 (m-30) cc_final: 0.7971 (m-30) REVERT: A 409 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8375 (ptm160) REVERT: A 455 LEU cc_start: 0.9005 (mt) cc_final: 0.8456 (mm) REVERT: A 458 MET cc_start: 0.8099 (mmm) cc_final: 0.7454 (tmm) REVERT: A 481 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: B 51 ASP cc_start: 0.8327 (t0) cc_final: 0.8115 (t0) REVERT: B 79 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7476 (mtm180) REVERT: B 133 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 135 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 141 ASN cc_start: 0.8666 (m-40) cc_final: 0.8311 (m-40) REVERT: B 155 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8047 (ptm-80) REVERT: B 284 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8189 (mtmm) REVERT: B 342 MET cc_start: 0.5197 (ttp) cc_final: 0.4744 (ttp) REVERT: B 345 TRP cc_start: 0.6900 (m100) cc_final: 0.6677 (m100) REVERT: B 371 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 376 GLU cc_start: 0.8139 (tt0) cc_final: 0.7906 (tt0) REVERT: B 458 MET cc_start: 0.8305 (mmt) cc_final: 0.7894 (mmp) REVERT: C 10 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7019 (t) REVERT: C 21 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7774 (tpp80) REVERT: C 24 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 46 VAL cc_start: 0.8700 (t) cc_final: 0.8459 (p) REVERT: C 54 ASP cc_start: 0.8240 (t0) cc_final: 0.7805 (t0) REVERT: C 56 LYS cc_start: 0.8039 (tppp) cc_final: 0.7833 (tppp) REVERT: C 79 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7680 (mtp85) REVERT: C 92 GLN cc_start: 0.8550 (mt0) cc_final: 0.8261 (mt0) REVERT: C 142 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8205 (ttp-110) REVERT: C 147 PHE cc_start: 0.8832 (t80) cc_final: 0.8505 (t80) REVERT: C 177 ASP cc_start: 0.7738 (t0) cc_final: 0.7412 (t0) REVERT: C 186 GLU cc_start: 0.8239 (tp30) cc_final: 0.7729 (tp30) REVERT: C 199 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.6958 (p-80) REVERT: C 208 ARG cc_start: 0.8743 (mpp80) cc_final: 0.8296 (mtm-85) REVERT: C 220 LEU cc_start: 0.8839 (tt) cc_final: 0.8601 (tp) REVERT: C 242 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7803 (mt-10) REVERT: C 279 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7799 (mtt180) REVERT: C 342 MET cc_start: 0.4856 (OUTLIER) cc_final: 0.4055 (mmm) REVERT: C 433 ARG cc_start: 0.7435 (tpt-90) cc_final: 0.7082 (mmm160) REVERT: C 459 ASN cc_start: 0.8457 (m-40) cc_final: 0.8116 (m110) REVERT: D 20 GLU cc_start: 0.7870 (mp0) cc_final: 0.7304 (mp0) REVERT: D 27 GLN cc_start: 0.8365 (mt0) cc_final: 0.8124 (mm110) REVERT: D 28 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 42 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: D 78 TYR cc_start: 0.8648 (t80) cc_final: 0.8313 (t80) REVERT: D 81 ASP cc_start: 0.8503 (p0) cc_final: 0.8223 (p0) REVERT: D 109 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7617 (mt-10) REVERT: D 154 TYR cc_start: 0.8573 (t80) cc_final: 0.8234 (t80) REVERT: D 173 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8113 (mtp180) REVERT: D 179 VAL cc_start: 0.7735 (OUTLIER) cc_final: 0.7484 (p) REVERT: D 182 GLU cc_start: 0.7603 (tt0) cc_final: 0.6908 (tm-30) REVERT: D 186 GLU cc_start: 0.8158 (tt0) cc_final: 0.7902 (tt0) REVERT: D 204 ASP cc_start: 0.8248 (t70) cc_final: 0.7898 (t0) REVERT: D 219 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7473 (tt0) REVERT: D 265 ARG cc_start: 0.8416 (ptt180) cc_final: 0.8201 (ptt180) REVERT: D 329 MET cc_start: 0.8051 (tpp) cc_final: 0.7721 (tpp) REVERT: D 348 PHE cc_start: 0.7966 (t80) cc_final: 0.7546 (t80) REVERT: D 351 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: D 409 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8431 (mmm160) outliers start: 59 outliers final: 41 residues processed: 435 average time/residue: 0.1567 time to fit residues: 98.9157 Evaluate side-chains 449 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 396 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 THR 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 272 ARG 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 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 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER 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 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 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 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 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=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: 2.9990 chunk 66 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 219 GLN A 352 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS ** 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 = 0.4204 r_free = 0.4204 target = 0.179419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127068 restraints weight = 46411.254| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.02 r_work: 0.3289 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3586 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= 0.169 Angle : 0.609 10.450 28386 Z= 0.338 Chirality : 0.042 0.240 3109 Planarity : 0.005 0.044 3022 Dihedral : 23.180 88.316 4296 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.05 % Allowed : 17.57 % Favored : 78.38 % 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: 2.29 (0.17), residues: 913 sheet: -0.26 (0.29), residues: 290 loop : 0.52 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.018 0.002 TYR C 396 PHE 0.037 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 0.00331 / 0.17 (20298) covalent geometry : angle 0.60248 / 0.34 (28362) hydrogen bonds : bond 0.04338 / 3.01 ( 1060) hydrogen bonds : angle 3.70968 / 2.66 ( 2790) metal coordination : bond 0.00508 / 0.30 ( 16) metal coordination : angle 3.10356 / 1.89 ( 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 469 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 404 time to evaluate : 0.374 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 27 GLN cc_start: 0.7856 (mt0) cc_final: 0.7559 (mt0) REVERT: A 28 GLN cc_start: 0.8542 (tt0) cc_final: 0.8254 (tt0) REVERT: A 64 TRP cc_start: 0.8252 (m-90) cc_final: 0.7878 (m-10) REVERT: A 69 GLU cc_start: 0.6584 (mp0) cc_final: 0.6174 (mp0) REVERT: A 82 ARG cc_start: 0.8082 (mmt180) cc_final: 0.7353 (mmp80) REVERT: A 84 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7829 (m) REVERT: A 98 GLU cc_start: 0.7350 (tp30) cc_final: 0.6857 (tp30) REVERT: A 100 HIS cc_start: 0.8026 (m170) cc_final: 0.7650 (m170) REVERT: A 137 ILE cc_start: 0.8575 (mt) cc_final: 0.8305 (tt) REVERT: A 147 PHE cc_start: 0.8697 (t80) cc_final: 0.8471 (t80) REVERT: A 155 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7402 (ptt90) REVERT: A 182 GLU cc_start: 0.7354 (tt0) cc_final: 0.7095 (tt0) REVERT: A 196 GLU cc_start: 0.8391 (pt0) cc_final: 0.8127 (pt0) REVERT: A 203 HIS cc_start: 0.7721 (t-90) cc_final: 0.7245 (t-90) REVERT: A 220 LEU cc_start: 0.8397 (mt) cc_final: 0.8069 (tt) REVERT: A 281 GLU cc_start: 0.8194 (tp30) cc_final: 0.7970 (tp30) REVERT: A 376 GLU cc_start: 0.8456 (tt0) cc_final: 0.8243 (tt0) REVERT: A 383 GLU cc_start: 0.8908 (tt0) cc_final: 0.8479 (tt0) REVERT: A 391 ILE cc_start: 0.6593 (mt) cc_final: 0.6388 (mt) REVERT: A 407 ASP cc_start: 0.8245 (m-30) cc_final: 0.7995 (m-30) REVERT: A 409 ARG cc_start: 0.8740 (ttp-170) cc_final: 0.8458 (ptm160) REVERT: A 455 LEU cc_start: 0.8984 (mt) cc_final: 0.8413 (mm) REVERT: A 458 MET cc_start: 0.8110 (mmm) cc_final: 0.7454 (tmm) REVERT: A 481 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: B 51 ASP cc_start: 0.8278 (t0) cc_final: 0.8067 (t0) REVERT: B 68 GLU cc_start: 0.7268 (pt0) cc_final: 0.6794 (pp20) REVERT: B 79 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7303 (mtm180) REVERT: B 133 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 135 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 141 ASN cc_start: 0.8583 (m-40) cc_final: 0.8222 (m-40) REVERT: B 155 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8000 (ptm-80) REVERT: B 257 ASP cc_start: 0.7439 (t70) cc_final: 0.7220 (t70) REVERT: B 284 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8075 (mtmm) REVERT: B 342 MET cc_start: 0.5085 (ttp) cc_final: 0.4613 (ttp) REVERT: B 371 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 376 GLU cc_start: 0.8105 (tt0) cc_final: 0.7865 (tt0) REVERT: B 458 MET cc_start: 0.8244 (mmt) cc_final: 0.7810 (mmp) REVERT: C 10 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.6875 (t) REVERT: C 21 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7670 (tpp80) REVERT: C 24 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 46 VAL cc_start: 0.8632 (t) cc_final: 0.8396 (p) REVERT: C 54 ASP cc_start: 0.8143 (t0) cc_final: 0.7757 (t0) REVERT: C 69 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7672 (mm-30) REVERT: C 92 GLN cc_start: 0.8299 (mt0) cc_final: 0.8025 (mt0) REVERT: C 135 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C 142 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7968 (ttp-110) REVERT: C 147 PHE cc_start: 0.8768 (t80) cc_final: 0.8433 (t80) REVERT: C 177 ASP cc_start: 0.7496 (t0) cc_final: 0.7159 (t0) REVERT: C 186 GLU cc_start: 0.8112 (tp30) cc_final: 0.7775 (tp30) REVERT: C 199 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6879 (p-80) REVERT: C 208 ARG cc_start: 0.8546 (mpp80) cc_final: 0.8122 (mtm-85) REVERT: C 220 LEU cc_start: 0.8769 (tt) cc_final: 0.8363 (tt) REVERT: C 240 ILE cc_start: 0.8276 (mm) cc_final: 0.7586 (tt) REVERT: C 242 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7589 (mt-10) REVERT: C 279 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7565 (mtt180) REVERT: C 342 MET cc_start: 0.4782 (OUTLIER) cc_final: 0.3980 (mmm) REVERT: C 433 ARG cc_start: 0.7477 (tpt-90) cc_final: 0.7104 (mmm160) REVERT: C 459 ASN cc_start: 0.8436 (m-40) cc_final: 0.8089 (m110) REVERT: C 461 ARG cc_start: 0.6955 (mtp180) cc_final: 0.6680 (mtp180) REVERT: D 20 GLU cc_start: 0.7665 (mp0) cc_final: 0.7139 (mp0) REVERT: D 27 GLN cc_start: 0.8174 (mt0) cc_final: 0.7964 (mm110) REVERT: D 28 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7337 (tm-30) REVERT: D 42 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: D 78 TYR cc_start: 0.8543 (t80) cc_final: 0.8178 (t80) REVERT: D 109 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7451 (mt-10) REVERT: D 118 PHE cc_start: 0.8384 (m-10) cc_final: 0.8072 (m-10) REVERT: D 154 TYR cc_start: 0.8519 (t80) cc_final: 0.8193 (t80) REVERT: D 179 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7364 (p) REVERT: D 182 GLU cc_start: 0.7242 (tt0) cc_final: 0.6652 (tm-30) REVERT: D 186 GLU cc_start: 0.7939 (tt0) cc_final: 0.7727 (tt0) REVERT: D 204 ASP cc_start: 0.8035 (t70) cc_final: 0.7658 (t0) REVERT: D 219 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7322 (tt0) REVERT: D 226 GLN cc_start: 0.8237 (mm110) cc_final: 0.7999 (mm110) REVERT: D 329 MET cc_start: 0.7919 (tpp) cc_final: 0.7592 (tpp) REVERT: D 409 ARG cc_start: 0.8728 (mmm160) cc_final: 0.8402 (mmm160) outliers start: 65 outliers final: 45 residues processed: 435 average time/residue: 0.1613 time to fit residues: 102.1409 Evaluate side-chains 458 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 401 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 THR 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 272 ARG 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 69 GLU 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 192 VAL 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 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 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 224 GLU Chi-restraints excluded: chain C residue 329 MET 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 200 LEU Chi-restraints excluded: chain D residue 205 LEU 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: 0.0770 chunk 16 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 22 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 126 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 219 GLN A 226 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS ** 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 = 0.4198 r_free = 0.4198 target = 0.178829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127603 restraints weight = 36960.884| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.63 r_work: 0.3312 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20314 Z= 0.206 Angle : 0.629 10.900 28386 Z= 0.350 Chirality : 0.043 0.231 3109 Planarity : 0.005 0.067 3022 Dihedral : 23.189 88.326 4295 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.68 % Allowed : 18.50 % 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: 1.72 (0.19), residues: 1937 helix: 2.22 (0.17), residues: 913 sheet: -0.29 (0.29), residues: 290 loop : 0.49 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 300 TYR 0.019 0.002 TYR D 324 PHE 0.043 0.002 PHE D 348 TRP 0.035 0.001 TRP B 345 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (20298) covalent geometry : angle 0.62298 / 0.35 (28362) hydrogen bonds : bond 0.04446 / 3.09 ( 1060) hydrogen bonds : angle 3.75690 / 2.69 ( 2790) metal coordination : bond 0.00569 / 0.33 ( 16) metal coordination : angle 2.97587 / 1.82 ( 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: 59 poor density : 409 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: A 27 GLN cc_start: 0.7830 (mt0) cc_final: 0.7527 (mt0) REVERT: A 28 GLN cc_start: 0.8491 (tt0) cc_final: 0.8208 (tt0) REVERT: A 64 TRP cc_start: 0.8269 (m-90) cc_final: 0.7899 (m-10) REVERT: A 69 GLU cc_start: 0.6443 (mp0) cc_final: 0.6068 (mp0) REVERT: A 82 ARG cc_start: 0.8067 (mmt180) cc_final: 0.7345 (mmp80) REVERT: A 84 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7948 (m) REVERT: A 98 GLU cc_start: 0.7302 (tp30) cc_final: 0.6816 (tp30) REVERT: A 100 HIS cc_start: 0.8016 (m170) cc_final: 0.7648 (m170) REVERT: A 137 ILE cc_start: 0.8555 (mt) cc_final: 0.8276 (tt) REVERT: A 147 PHE cc_start: 0.8665 (t80) cc_final: 0.8426 (t80) REVERT: A 155 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7369 (ptt90) REVERT: A 182 GLU cc_start: 0.7330 (tt0) cc_final: 0.7068 (tt0) REVERT: A 203 HIS cc_start: 0.7697 (t-90) cc_final: 0.7220 (t-90) REVERT: A 220 LEU cc_start: 0.8404 (mt) cc_final: 0.8074 (tt) REVERT: A 281 GLU cc_start: 0.8198 (tp30) cc_final: 0.7946 (tp30) REVERT: A 342 MET cc_start: 0.5270 (ttp) cc_final: 0.4952 (ttp) REVERT: A 376 GLU cc_start: 0.8408 (tt0) cc_final: 0.8166 (tt0) REVERT: A 383 GLU cc_start: 0.8866 (tt0) cc_final: 0.8430 (tt0) REVERT: A 407 ASP cc_start: 0.8229 (m-30) cc_final: 0.7984 (m-30) REVERT: A 409 ARG cc_start: 0.8721 (ttp-170) cc_final: 0.8438 (ptm160) REVERT: A 455 LEU cc_start: 0.9009 (mt) cc_final: 0.8584 (mm) REVERT: A 458 MET cc_start: 0.8086 (mmm) cc_final: 0.7150 (tmm) REVERT: A 481 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: B 51 ASP cc_start: 0.8300 (t0) cc_final: 0.8073 (t0) REVERT: B 68 GLU cc_start: 0.7165 (pt0) cc_final: 0.6773 (pp20) REVERT: B 79 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7326 (mtm180) REVERT: B 133 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 135 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 141 ASN cc_start: 0.8578 (m-40) cc_final: 0.8213 (m-40) REVERT: B 155 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7948 (ptm-80) REVERT: B 257 ASP cc_start: 0.7460 (t70) cc_final: 0.7244 (t70) REVERT: B 284 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8076 (mtmm) REVERT: B 342 MET cc_start: 0.4949 (ttp) cc_final: 0.4535 (ttp) REVERT: B 371 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 376 GLU cc_start: 0.8086 (tt0) cc_final: 0.7851 (tt0) REVERT: B 458 MET cc_start: 0.8214 (mmt) cc_final: 0.7784 (mmp) REVERT: C 10 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.6966 (t) REVERT: C 21 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7646 (tpp80) REVERT: C 24 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 46 VAL cc_start: 0.8637 (t) cc_final: 0.8386 (p) REVERT: C 54 ASP cc_start: 0.8120 (t0) cc_final: 0.7718 (t0) REVERT: C 69 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: C 92 GLN cc_start: 0.8272 (mt0) cc_final: 0.7985 (mt0) REVERT: C 135 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7758 (mm-30) REVERT: C 142 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7925 (ttp-110) REVERT: C 147 PHE cc_start: 0.8766 (t80) cc_final: 0.8456 (t80) REVERT: C 177 ASP cc_start: 0.7412 (t0) cc_final: 0.7096 (t0) REVERT: C 186 GLU cc_start: 0.8092 (tp30) cc_final: 0.7759 (tp30) REVERT: C 199 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6882 (p-80) REVERT: C 208 ARG cc_start: 0.8497 (mpp80) cc_final: 0.8088 (mtm-85) REVERT: C 220 LEU cc_start: 0.8766 (tt) cc_final: 0.8355 (tt) REVERT: C 242 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7576 (mt-10) REVERT: C 279 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7540 (mtt180) REVERT: C 300 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7718 (mmt-90) REVERT: C 342 MET cc_start: 0.4774 (OUTLIER) cc_final: 0.3969 (mmm) REVERT: C 433 ARG cc_start: 0.7449 (tpt-90) cc_final: 0.7081 (mmm160) REVERT: C 459 ASN cc_start: 0.8461 (m-40) cc_final: 0.8125 (m110) REVERT: C 461 ARG cc_start: 0.7008 (mtp180) cc_final: 0.6598 (mtp85) REVERT: D 20 GLU cc_start: 0.7644 (mp0) cc_final: 0.7118 (mp0) REVERT: D 22 GLN cc_start: 0.8155 (mt0) cc_final: 0.7953 (mt0) REVERT: D 27 GLN cc_start: 0.8151 (mt0) cc_final: 0.7943 (mm110) REVERT: D 28 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7284 (tm-30) REVERT: D 42 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: D 78 TYR cc_start: 0.8515 (t80) cc_final: 0.8143 (t80) REVERT: D 109 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7415 (mt-10) REVERT: D 118 PHE cc_start: 0.8380 (m-10) cc_final: 0.8060 (m-10) REVERT: D 154 TYR cc_start: 0.8510 (t80) cc_final: 0.8217 (t80) REVERT: D 173 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7968 (mtp180) REVERT: D 182 GLU cc_start: 0.7175 (tt0) cc_final: 0.6625 (tm-30) REVERT: D 204 ASP cc_start: 0.8021 (t70) cc_final: 0.7640 (t0) REVERT: D 219 GLN cc_start: 0.7611 (tp-100) cc_final: 0.7294 (tt0) REVERT: D 226 GLN cc_start: 0.8210 (mm110) cc_final: 0.7975 (mm110) REVERT: D 329 MET cc_start: 0.7895 (tpp) cc_final: 0.7582 (tpp) REVERT: D 351 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: D 409 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8343 (mmm160) outliers start: 59 outliers final: 41 residues processed: 438 average time/residue: 0.1746 time to fit residues: 110.8958 Evaluate side-chains 458 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 405 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 THR 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 272 ARG 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 69 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER 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 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 329 MET 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 296 SER 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 113 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 219 GLN B 199 HIS B 274 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.180146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129398 restraints weight = 35581.800| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.59 r_work: 0.3340 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 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: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20314 Z= 0.146 Angle : 0.608 11.151 28386 Z= 0.341 Chirality : 0.041 0.224 3109 Planarity : 0.005 0.042 3022 Dihedral : 23.164 88.573 4293 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.30 % Allowed : 19.50 % 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: 1.84 (0.20), residues: 1937 helix: 2.33 (0.17), residues: 912 sheet: -0.35 (0.29), residues: 286 loop : 0.59 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 409 TYR 0.018 0.002 TYR C 396 PHE 0.044 0.002 PHE C 314 TRP 0.065 0.001 TRP B 345 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (20298) covalent geometry : angle 0.60222 / 0.34 (28362) hydrogen bonds : bond 0.04174 / 2.91 ( 1060) hydrogen bonds : angle 3.70884 / 2.65 ( 2790) metal coordination : bond 0.00373 / 0.23 ( 16) metal coordination : angle 3.01739 / 1.81 ( 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 463 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 410 time to evaluate : 0.676 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: A 27 GLN cc_start: 0.7821 (mt0) cc_final: 0.7508 (mt0) REVERT: A 28 GLN cc_start: 0.8524 (tt0) cc_final: 0.8235 (tt0) REVERT: A 82 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7250 (mmp80) REVERT: A 98 GLU cc_start: 0.7300 (tp30) cc_final: 0.6800 (tp30) REVERT: A 100 HIS cc_start: 0.8002 (m170) cc_final: 0.7619 (m170) REVERT: A 137 ILE cc_start: 0.8558 (mt) cc_final: 0.8286 (tt) REVERT: A 147 PHE cc_start: 0.8672 (t80) cc_final: 0.8437 (t80) REVERT: A 155 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7331 (ptt90) REVERT: A 164 LEU cc_start: 0.8220 (mm) cc_final: 0.7980 (mt) REVERT: A 182 GLU cc_start: 0.7196 (tt0) cc_final: 0.6937 (tt0) REVERT: A 196 GLU cc_start: 0.8220 (pt0) cc_final: 0.7867 (pt0) REVERT: A 203 HIS cc_start: 0.7663 (t-90) cc_final: 0.7187 (t-90) REVERT: A 220 LEU cc_start: 0.8458 (mt) cc_final: 0.8173 (tp) REVERT: A 281 GLU cc_start: 0.8167 (tp30) cc_final: 0.7908 (tp30) REVERT: A 342 MET cc_start: 0.5137 (ttp) cc_final: 0.4834 (ttp) REVERT: A 376 GLU cc_start: 0.8370 (tt0) cc_final: 0.8113 (tt0) REVERT: A 383 GLU cc_start: 0.8866 (tt0) cc_final: 0.8430 (tt0) REVERT: A 407 ASP cc_start: 0.8159 (m-30) cc_final: 0.7911 (m-30) REVERT: A 409 ARG cc_start: 0.8668 (ttp-170) cc_final: 0.8329 (ptm160) REVERT: A 455 LEU cc_start: 0.8994 (mt) cc_final: 0.8652 (mp) REVERT: A 458 MET cc_start: 0.8033 (mmm) cc_final: 0.7122 (tmm) REVERT: A 481 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: B 51 ASP cc_start: 0.8279 (t0) cc_final: 0.8065 (t0) REVERT: B 79 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7218 (mtm180) REVERT: B 133 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 135 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 141 ASN cc_start: 0.8579 (m-40) cc_final: 0.8337 (m-40) REVERT: B 155 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7900 (ptm-80) REVERT: B 257 ASP cc_start: 0.7418 (t70) cc_final: 0.7197 (t70) REVERT: B 284 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8037 (mtmm) REVERT: B 342 MET cc_start: 0.4781 (ttp) cc_final: 0.4367 (ttp) REVERT: B 371 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8169 (p) REVERT: B 376 GLU cc_start: 0.8074 (tt0) cc_final: 0.7833 (tt0) REVERT: B 458 MET cc_start: 0.8203 (mmt) cc_final: 0.7805 (mmp) REVERT: C 10 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.6730 (t) REVERT: C 21 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7553 (tpp80) REVERT: C 24 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7557 (tm-30) REVERT: C 46 VAL cc_start: 0.8592 (t) cc_final: 0.8377 (p) REVERT: C 54 ASP cc_start: 0.8112 (t0) cc_final: 0.7685 (t0) REVERT: C 69 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: C 79 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7493 (mtm-85) REVERT: C 92 GLN cc_start: 0.8216 (mt0) cc_final: 0.7894 (mt0) REVERT: C 135 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7741 (mm-30) REVERT: C 142 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7903 (ttp-110) REVERT: C 147 PHE cc_start: 0.8743 (t80) cc_final: 0.8389 (t80) REVERT: C 177 ASP cc_start: 0.7375 (t0) cc_final: 0.7064 (t0) REVERT: C 186 GLU cc_start: 0.8041 (tp30) cc_final: 0.7726 (tp30) REVERT: C 199 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6847 (p-80) REVERT: C 208 ARG cc_start: 0.8434 (mpp80) cc_final: 0.8043 (mtm-85) REVERT: C 220 LEU cc_start: 0.8739 (tt) cc_final: 0.8317 (tt) REVERT: C 240 ILE cc_start: 0.8194 (mm) cc_final: 0.7628 (tp) REVERT: C 242 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 279 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7475 (mtt180) REVERT: C 300 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7652 (mmt-90) REVERT: C 342 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.3941 (mmm) REVERT: C 409 ARG cc_start: 0.8484 (mmp80) cc_final: 0.8269 (mmt-90) REVERT: C 433 ARG cc_start: 0.7460 (tpt-90) cc_final: 0.7090 (mmm160) REVERT: C 459 ASN cc_start: 0.8431 (m-40) cc_final: 0.8109 (m110) REVERT: C 461 ARG cc_start: 0.6983 (mtp180) cc_final: 0.6771 (mtp180) REVERT: D 20 GLU cc_start: 0.7574 (mp0) cc_final: 0.7076 (mp0) REVERT: D 22 GLN cc_start: 0.8153 (mt0) cc_final: 0.7936 (mt0) REVERT: D 28 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 42 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: D 78 TYR cc_start: 0.8512 (t80) cc_final: 0.8149 (t80) REVERT: D 109 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7410 (mt-10) REVERT: D 118 PHE cc_start: 0.8370 (m-10) cc_final: 0.8032 (m-10) REVERT: D 154 TYR cc_start: 0.8486 (t80) cc_final: 0.8173 (t80) REVERT: D 173 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7936 (mtp180) REVERT: D 182 GLU cc_start: 0.7086 (tt0) cc_final: 0.6543 (tm-30) REVERT: D 204 ASP cc_start: 0.7972 (t70) cc_final: 0.7574 (t0) REVERT: D 219 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7266 (tt0) REVERT: D 229 GLU cc_start: 0.7467 (pp20) cc_final: 0.7169 (pp20) REVERT: D 329 MET cc_start: 0.7798 (tpp) cc_final: 0.7478 (tpp) REVERT: D 351 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7385 (pp20) REVERT: D 409 ARG cc_start: 0.8685 (mmm160) cc_final: 0.8344 (mmm160) outliers start: 53 outliers final: 37 residues processed: 435 average time/residue: 0.1722 time to fit residues: 108.8860 Evaluate side-chains 456 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 408 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain A residue 272 ARG 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 69 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 SER 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 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 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 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 351 GLU Chi-restraints excluded: chain D residue 352 GLN 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: 0.6980 chunk 98 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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** C 219 GLN ** C 352 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 = 0.4211 r_free = 0.4211 target = 0.179840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129163 restraints weight = 34891.564| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.56 r_work: 0.3343 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 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: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 20314 Z= 0.216 Angle : 0.761 59.199 28386 Z= 0.449 Chirality : 0.044 0.947 3109 Planarity : 0.005 0.042 3022 Dihedral : 23.162 88.591 4293 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.30 % Allowed : 19.31 % Favored : 77.38 % Cbeta Deviations : 0.06 % 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: 1.84 (0.19), residues: 1937 helix: 2.33 (0.17), residues: 912 sheet: -0.35 (0.29), residues: 286 loop : 0.59 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 2 TYR 0.016 0.002 TYR D 188 PHE 0.037 0.002 PHE C 314 TRP 0.056 0.001 TRP B 345 HIS 0.012 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.22 (20298) covalent geometry : angle 0.75604 / 0.45 (28362) hydrogen bonds : bond 0.04185 / 2.92 ( 1060) hydrogen bonds : angle 3.71070 / 2.65 ( 2790) metal coordination : bond 0.00381 / 0.23 ( 16) metal coordination : angle 3.00632 / 1.80 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6508.45 seconds wall clock time: 111 minutes 11.48 seconds (6671.48 seconds total)