Starting phenix.real_space_refine on Thu Sep 18 04:24:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ekt_48136/09_2025/9ekt_48136.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ekt_48136/09_2025/9ekt_48136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ekt_48136/09_2025/9ekt_48136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ekt_48136/09_2025/9ekt_48136.map" model { file = "/net/cci-nas-00/data/ceres_data/9ekt_48136/09_2025/9ekt_48136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ekt_48136/09_2025/9ekt_48136.cif" } resolution = 2.35 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= 0.023 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9200 2.51 5 N 2308 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14052 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3513 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 12, 'TRANS': 426} Chain breaks: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 2.23, per 1000 atoms: 0.16 Number of scatterers: 14052 At special positions: 0 Unit cell: (111.438, 110.7, 107.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2452 8.00 N 2308 7.00 C 9200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.03 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: 1.12 Conformation dependent library (CDL) restraints added in 571.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 63.3% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.793A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 297 through 335 removed outlier: 4.091A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 407 removed outlier: 3.881A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 448 removed outlier: 3.868A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.952A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.850A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 473 through 482 Processing helix chain 'A' and resid 487 through 526 removed outlier: 4.174A pdb=" N LEU A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 511 " --> pdb=" O TYR A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.792A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 297 through 335 removed outlier: 4.091A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 407 removed outlier: 3.881A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 448 removed outlier: 3.868A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.952A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.850A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 473 through 482 Processing helix chain 'B' and resid 487 through 526 removed outlier: 4.174A pdb=" N LEU B 510 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER B 511 " --> pdb=" O TYR B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.793A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 297 through 335 removed outlier: 4.090A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 407 removed outlier: 3.881A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 448 removed outlier: 3.869A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.952A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.850A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'C' and resid 473 through 482 Processing helix chain 'C' and resid 487 through 526 removed outlier: 4.174A pdb=" N LEU C 510 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER C 511 " --> pdb=" O TYR C 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.793A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 297 through 335 removed outlier: 4.092A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 407 removed outlier: 3.881A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 448 removed outlier: 3.869A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.952A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 3.850A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 473 through 482 Processing helix chain 'D' and resid 487 through 526 removed outlier: 4.174A pdb=" N LEU D 510 " --> pdb=" O ILE D 506 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER D 511 " --> pdb=" O TYR D 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.740A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.740A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLY A 173 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP A 185 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL A 175 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP A 183 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 182 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 288 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 184 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.072A pdb=" N HIS A 286 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE D 184 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER A 288 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP D 183 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL D 175 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP D 252 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.072A pdb=" N HIS A 286 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE D 184 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER A 288 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP D 183 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL D 175 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.740A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.740A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N MET B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLY B 173 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP B 185 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL B 175 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP B 183 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 182 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER C 288 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 184 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.739A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.739A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLY C 173 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP C 185 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL C 175 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP C 183 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 182 " --> pdb=" O HIS D 286 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER D 288 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 184 " --> pdb=" O SER D 288 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4364 1.34 - 1.46: 3652 1.46 - 1.58: 6248 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 14392 Sorted by residual: bond pdb=" N ILE A 524 " pdb=" CA ILE A 524 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.87e+00 bond pdb=" N ILE C 524 " pdb=" CA ILE C 524 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.77e+00 bond pdb=" N ILE D 524 " pdb=" CA ILE D 524 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.73e+00 bond pdb=" N ILE B 524 " pdb=" CA ILE B 524 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.52e+00 bond pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.35e-02 5.49e+03 6.50e+00 ... (remaining 14387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18756 1.26 - 2.52: 601 2.52 - 3.79: 142 3.79 - 5.05: 29 5.05 - 6.31: 16 Bond angle restraints: 19544 Sorted by residual: angle pdb=" CA THR B 518 " pdb=" CB THR B 518 " pdb=" OG1 THR B 518 " ideal model delta sigma weight residual 109.60 103.29 6.31 1.50e+00 4.44e-01 1.77e+01 angle pdb=" CA THR C 518 " pdb=" CB THR C 518 " pdb=" OG1 THR C 518 " ideal model delta sigma weight residual 109.60 103.32 6.28 1.50e+00 4.44e-01 1.75e+01 angle pdb=" CA THR A 518 " pdb=" CB THR A 518 " pdb=" OG1 THR A 518 " ideal model delta sigma weight residual 109.60 103.33 6.27 1.50e+00 4.44e-01 1.74e+01 angle pdb=" CA THR D 518 " pdb=" CB THR D 518 " pdb=" OG1 THR D 518 " ideal model delta sigma weight residual 109.60 103.36 6.24 1.50e+00 4.44e-01 1.73e+01 angle pdb=" CA THR C 523 " pdb=" CB THR C 523 " pdb=" OG1 THR C 523 " ideal model delta sigma weight residual 109.60 103.98 5.62 1.50e+00 4.44e-01 1.40e+01 ... (remaining 19539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 7313 17.62 - 35.25: 791 35.25 - 52.87: 208 52.87 - 70.50: 60 70.50 - 88.12: 8 Dihedral angle restraints: 8380 sinusoidal: 3252 harmonic: 5128 Sorted by residual: dihedral pdb=" CB CYS D 253 " pdb=" SG CYS D 253 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual 93.00 128.92 -35.92 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS B 253 " pdb=" SG CYS B 253 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual 93.00 128.92 -35.92 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 253 " pdb=" SG CYS A 253 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual 93.00 128.91 -35.91 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 8377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1282 0.025 - 0.051: 597 0.051 - 0.076: 226 0.076 - 0.102: 107 0.102 - 0.127: 56 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA ILE D 246 " pdb=" N ILE D 246 " pdb=" C ILE D 246 " pdb=" CB ILE D 246 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE A 246 " pdb=" N ILE A 246 " pdb=" C ILE A 246 " pdb=" CB ILE A 246 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE B 246 " pdb=" N ILE B 246 " pdb=" C ILE B 246 " pdb=" CB ILE B 246 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 2265 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 183 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C ASP C 183 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP C 183 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE C 184 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 183 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ASP D 183 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP D 183 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE D 184 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 183 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C ASP B 183 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP B 183 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 184 " -0.012 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 323 2.72 - 3.26: 13966 3.26 - 3.81: 23222 3.81 - 4.35: 28764 4.35 - 4.90: 47797 Nonbonded interactions: 114072 Sorted by model distance: nonbonded pdb=" OG1 THR D 365 " pdb=" OG SER D 393 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR B 365 " pdb=" OG SER B 393 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OG SER A 393 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR C 365 " pdb=" OG SER C 393 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASP A 384 " pdb=" OH TYR D 450 " model vdw 2.255 3.040 ... (remaining 114067 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.003 0.040 14400 Z= 0.197 Angle : 0.580 6.309 19560 Z= 0.355 Chirality : 0.039 0.127 2268 Planarity : 0.004 0.040 2412 Dihedral : 16.226 88.120 5052 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.64 % Allowed : 16.97 % Favored : 82.39 % 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 aren not related in a simple way. whole: 1.61 (0.20), residues: 1724 helix: 2.49 (0.16), residues: 1012 sheet: 0.13 (0.32), residues: 252 loop : -1.75 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 270 TYR 0.019 0.001 TYR B 521 PHE 0.016 0.001 PHE C 474 TRP 0.009 0.001 TRP D 444 HIS 0.003 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00332 (14392) covalent geometry : angle 0.57945 (19544) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.84096 ( 16) hydrogen bonds : bond 0.14198 ( 992) hydrogen bonds : angle 5.62764 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.581 Fit side-chains REVERT: A 300 LEU cc_start: 0.7665 (mt) cc_final: 0.6895 (tp) REVERT: A 419 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.7207 (ttm110) REVERT: B 65 LYS cc_start: 0.7491 (mttt) cc_final: 0.7206 (mptt) REVERT: C 65 LYS cc_start: 0.7493 (mttt) cc_final: 0.7211 (mptt) REVERT: C 286 HIS cc_start: 0.7832 (m90) cc_final: 0.7100 (m-70) REVERT: D 65 LYS cc_start: 0.7550 (mttt) cc_final: 0.7279 (mptt) outliers start: 10 outliers final: 5 residues processed: 203 average time/residue: 0.5490 time to fit residues: 122.8851 Evaluate side-chains 151 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101936 restraints weight = 15568.408| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.99 r_work: 0.3075 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14400 Z= 0.214 Angle : 0.615 7.078 19560 Z= 0.340 Chirality : 0.044 0.143 2268 Planarity : 0.005 0.044 2412 Dihedral : 4.748 22.334 1909 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.15 % Allowed : 15.17 % Favored : 81.68 % 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 aren not related in a simple way. whole: 1.58 (0.20), residues: 1724 helix: 2.42 (0.16), residues: 1016 sheet: 0.19 (0.33), residues: 252 loop : -1.75 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 298 TYR 0.013 0.002 TYR A 497 PHE 0.020 0.002 PHE A 182 TRP 0.010 0.002 TRP A 491 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00499 (14392) covalent geometry : angle 0.61349 (19544) SS BOND : bond 0.00399 ( 8) SS BOND : angle 1.53287 ( 16) hydrogen bonds : bond 0.07335 ( 992) hydrogen bonds : angle 4.49669 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 300 LEU cc_start: 0.7372 (mt) cc_final: 0.6598 (tp) REVERT: A 330 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.5234 (t80) REVERT: A 419 ARG cc_start: 0.7309 (ttp-110) cc_final: 0.6693 (ttm170) REVERT: B 66 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7266 (mm) REVERT: B 67 MET cc_start: 0.7136 (mmm) cc_final: 0.6903 (tmm) REVERT: B 330 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.5300 (t80) REVERT: B 334 MET cc_start: 0.3261 (pp-130) cc_final: 0.1095 (mtm) REVERT: B 383 TYR cc_start: 0.7700 (m-80) cc_final: 0.7457 (m-80) REVERT: C 66 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7259 (mm) REVERT: C 67 MET cc_start: 0.7116 (mmm) cc_final: 0.6875 (tmm) REVERT: C 330 PHE cc_start: 0.5533 (OUTLIER) cc_final: 0.5280 (t80) REVERT: C 334 MET cc_start: 0.3298 (pp-130) cc_final: 0.1075 (mtm) REVERT: C 383 TYR cc_start: 0.7714 (m-80) cc_final: 0.7479 (m-80) REVERT: D 88 GLN cc_start: 0.7786 (pt0) cc_final: 0.6992 (tp40) REVERT: D 330 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.5304 (t80) REVERT: D 334 MET cc_start: 0.3264 (pp-130) cc_final: 0.1164 (mtm) REVERT: D 383 TYR cc_start: 0.7707 (m-80) cc_final: 0.7424 (m-80) outliers start: 49 outliers final: 14 residues processed: 219 average time/residue: 0.5089 time to fit residues: 124.5040 Evaluate side-chains 180 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 359 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099464 restraints weight = 15751.127| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.98 r_work: 0.3017 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14400 Z= 0.225 Angle : 0.619 7.303 19560 Z= 0.341 Chirality : 0.045 0.148 2268 Planarity : 0.004 0.044 2412 Dihedral : 4.833 23.582 1906 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.65 % Favored : 96.11 % Rotamer: Outliers : 5.40 % Allowed : 12.15 % Favored : 82.46 % 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 aren not related in a simple way. whole: 1.46 (0.20), residues: 1724 helix: 2.32 (0.16), residues: 1016 sheet: -0.05 (0.32), residues: 252 loop : -1.63 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 298 TYR 0.012 0.002 TYR A 497 PHE 0.017 0.002 PHE B 474 TRP 0.011 0.002 TRP B 398 HIS 0.004 0.001 HIS D 234 Details of bonding type rmsd covalent geometry : bond 0.00534 (14392) covalent geometry : angle 0.61715 (19544) SS BOND : bond 0.00465 ( 8) SS BOND : angle 1.56606 ( 16) hydrogen bonds : bond 0.07509 ( 992) hydrogen bonds : angle 4.51590 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 181 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8163 (m-40) cc_final: 0.7770 (m-40) REVERT: A 182 PHE cc_start: 0.8597 (p90) cc_final: 0.8363 (p90) REVERT: A 300 LEU cc_start: 0.7600 (mt) cc_final: 0.6857 (tp) REVERT: A 330 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.5514 (t80) REVERT: A 419 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.6954 (ttm170) REVERT: B 67 MET cc_start: 0.7347 (mmm) cc_final: 0.7007 (ttt) REVERT: B 159 ASN cc_start: 0.8139 (m-40) cc_final: 0.7706 (m-40) REVERT: B 283 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: B 300 LEU cc_start: 0.7422 (mt) cc_final: 0.6655 (tp) REVERT: B 330 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5766 (t80) REVERT: B 334 MET cc_start: 0.3838 (OUTLIER) cc_final: 0.1709 (mtt) REVERT: C 67 MET cc_start: 0.7339 (mmm) cc_final: 0.6996 (ttt) REVERT: C 159 ASN cc_start: 0.8142 (m-40) cc_final: 0.7713 (m-40) REVERT: C 300 LEU cc_start: 0.7437 (mt) cc_final: 0.6671 (tp) REVERT: C 330 PHE cc_start: 0.5998 (OUTLIER) cc_final: 0.5772 (t80) REVERT: C 334 MET cc_start: 0.3892 (OUTLIER) cc_final: 0.1724 (mtt) REVERT: D 159 ASN cc_start: 0.8156 (m-40) cc_final: 0.7721 (m-40) REVERT: D 283 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: D 300 LEU cc_start: 0.7425 (mt) cc_final: 0.6697 (tp) REVERT: D 330 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5662 (t80) REVERT: D 334 MET cc_start: 0.3704 (OUTLIER) cc_final: 0.1608 (mmm) outliers start: 84 outliers final: 25 residues processed: 236 average time/residue: 0.5331 time to fit residues: 139.5182 Evaluate side-chains 205 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 518 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103445 restraints weight = 15700.842| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.97 r_work: 0.3078 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14400 Z= 0.145 Angle : 0.515 5.935 19560 Z= 0.287 Chirality : 0.040 0.129 2268 Planarity : 0.004 0.045 2412 Dihedral : 4.527 21.098 1906 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.65 % Favored : 96.11 % Rotamer: Outliers : 2.83 % Allowed : 15.23 % Favored : 81.94 % 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 aren not related in a simple way. whole: 1.89 (0.21), residues: 1724 helix: 2.76 (0.16), residues: 1016 sheet: 0.01 (0.32), residues: 252 loop : -1.63 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.013 0.001 TYR D 497 PHE 0.014 0.001 PHE D 474 TRP 0.009 0.001 TRP A 398 HIS 0.003 0.000 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00312 (14392) covalent geometry : angle 0.51408 (19544) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.22937 ( 16) hydrogen bonds : bond 0.05968 ( 992) hydrogen bonds : angle 4.18420 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8137 (m-40) cc_final: 0.7737 (m-40) REVERT: A 182 PHE cc_start: 0.8583 (p90) cc_final: 0.8279 (p90) REVERT: A 300 LEU cc_start: 0.7504 (mt) cc_final: 0.6725 (tp) REVERT: A 330 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5413 (t80) REVERT: A 419 ARG cc_start: 0.7419 (ttp-110) cc_final: 0.6861 (ttm170) REVERT: A 480 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7994 (mmm) REVERT: B 67 MET cc_start: 0.7226 (mmm) cc_final: 0.6868 (ttt) REVERT: B 159 ASN cc_start: 0.8144 (m-40) cc_final: 0.7712 (m-40) REVERT: B 219 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7303 (mmpt) REVERT: B 300 LEU cc_start: 0.7353 (mt) cc_final: 0.6595 (tp) REVERT: B 311 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7511 (tp) REVERT: B 321 LEU cc_start: 0.7543 (tp) cc_final: 0.7343 (tt) REVERT: B 330 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5802 (t80) REVERT: B 334 MET cc_start: 0.3648 (pp-130) cc_final: 0.1570 (mtt) REVERT: B 480 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7982 (mmm) REVERT: C 67 MET cc_start: 0.7191 (mmm) cc_final: 0.6842 (ttt) REVERT: C 159 ASN cc_start: 0.8136 (m-40) cc_final: 0.7705 (m-40) REVERT: C 219 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7305 (mmpt) REVERT: C 300 LEU cc_start: 0.7349 (mt) cc_final: 0.6596 (tp) REVERT: C 311 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7540 (tp) REVERT: C 321 LEU cc_start: 0.7528 (tp) cc_final: 0.7322 (tt) REVERT: C 330 PHE cc_start: 0.5954 (OUTLIER) cc_final: 0.5753 (t80) REVERT: C 334 MET cc_start: 0.3732 (pp-130) cc_final: 0.1611 (mtt) REVERT: C 480 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7994 (mmm) REVERT: D 159 ASN cc_start: 0.8122 (m-40) cc_final: 0.7694 (m-40) REVERT: D 219 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7327 (mmpt) REVERT: D 300 LEU cc_start: 0.7341 (mt) cc_final: 0.6582 (tp) REVERT: D 311 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7552 (tp) REVERT: D 330 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5836 (t80) REVERT: D 334 MET cc_start: 0.3702 (pp-130) cc_final: 0.1644 (mtt) REVERT: D 480 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7995 (mmm) outliers start: 44 outliers final: 13 residues processed: 204 average time/residue: 0.5364 time to fit residues: 121.4009 Evaluate side-chains 207 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 518 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105146 restraints weight = 15706.784| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.96 r_work: 0.3104 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14400 Z= 0.134 Angle : 0.497 5.351 19560 Z= 0.277 Chirality : 0.040 0.128 2268 Planarity : 0.004 0.044 2412 Dihedral : 4.361 20.227 1904 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.07 % Favored : 96.69 % Rotamer: Outliers : 2.38 % Allowed : 16.00 % 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 aren not related in a simple way. whole: 2.02 (0.21), residues: 1724 helix: 2.87 (0.16), residues: 1016 sheet: 0.03 (0.33), residues: 252 loop : -1.59 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.014 0.001 TYR B 497 PHE 0.013 0.001 PHE C 474 TRP 0.009 0.001 TRP A 398 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00279 (14392) covalent geometry : angle 0.49643 (19544) SS BOND : bond 0.00299 ( 8) SS BOND : angle 1.12628 ( 16) hydrogen bonds : bond 0.05595 ( 992) hydrogen bonds : angle 4.07652 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7538 (mm) REVERT: A 159 ASN cc_start: 0.8155 (m-40) cc_final: 0.7744 (m-40) REVERT: A 182 PHE cc_start: 0.8599 (p90) cc_final: 0.8340 (p90) REVERT: A 300 LEU cc_start: 0.7470 (mt) cc_final: 0.6703 (tp) REVERT: A 330 PHE cc_start: 0.5699 (OUTLIER) cc_final: 0.5252 (t80) REVERT: A 419 ARG cc_start: 0.7405 (ttp-110) cc_final: 0.6864 (ttm170) REVERT: A 480 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7988 (mmm) REVERT: B 67 MET cc_start: 0.7112 (mmm) cc_final: 0.6737 (ttt) REVERT: B 159 ASN cc_start: 0.8152 (m-40) cc_final: 0.7710 (m-40) REVERT: B 300 LEU cc_start: 0.7414 (mt) cc_final: 0.6568 (tp) REVERT: B 311 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7476 (tp) REVERT: B 334 MET cc_start: 0.3719 (pp-130) cc_final: 0.1742 (mtt) REVERT: B 480 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7925 (mmm) REVERT: C 67 MET cc_start: 0.7087 (mmm) cc_final: 0.6725 (ttt) REVERT: C 159 ASN cc_start: 0.8147 (m-40) cc_final: 0.7709 (m-40) REVERT: C 300 LEU cc_start: 0.7409 (mt) cc_final: 0.6563 (tp) REVERT: C 311 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7510 (tp) REVERT: C 334 MET cc_start: 0.3693 (pp-130) cc_final: 0.1704 (mtt) REVERT: C 480 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7949 (mmm) REVERT: D 159 ASN cc_start: 0.8156 (m-40) cc_final: 0.7726 (m-40) REVERT: D 300 LEU cc_start: 0.7419 (mt) cc_final: 0.6564 (tp) REVERT: D 311 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7526 (tp) REVERT: D 334 MET cc_start: 0.3743 (pp-130) cc_final: 0.1764 (mtt) REVERT: D 480 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7934 (mmm) outliers start: 37 outliers final: 13 residues processed: 201 average time/residue: 0.5515 time to fit residues: 123.2022 Evaluate side-chains 206 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101130 restraints weight = 15692.859| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.00 r_work: 0.3042 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14400 Z= 0.177 Angle : 0.550 6.346 19560 Z= 0.305 Chirality : 0.042 0.133 2268 Planarity : 0.004 0.043 2412 Dihedral : 4.561 22.808 1904 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.54 % Favored : 96.29 % Rotamer: Outliers : 3.21 % Allowed : 15.04 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.20), residues: 1724 helix: 2.65 (0.16), residues: 1016 sheet: 0.03 (0.32), residues: 252 loop : -1.55 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.014 0.001 TYR C 497 PHE 0.014 0.001 PHE D 474 TRP 0.011 0.002 TRP C 398 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00401 (14392) covalent geometry : angle 0.54892 (19544) SS BOND : bond 0.00404 ( 8) SS BOND : angle 1.31707 ( 16) hydrogen bonds : bond 0.06585 ( 992) hydrogen bonds : angle 4.26692 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.581 Fit side-chains REVERT: A 159 ASN cc_start: 0.8209 (m-40) cc_final: 0.7799 (m-40) REVERT: A 182 PHE cc_start: 0.8577 (p90) cc_final: 0.8288 (p90) REVERT: A 300 LEU cc_start: 0.7513 (mt) cc_final: 0.6714 (tp) REVERT: A 419 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.6860 (ttm170) REVERT: B 67 MET cc_start: 0.7188 (mmm) cc_final: 0.6860 (ttt) REVERT: B 159 ASN cc_start: 0.8227 (m-40) cc_final: 0.7790 (m-40) REVERT: B 219 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7333 (mmpt) REVERT: B 300 LEU cc_start: 0.7437 (mt) cc_final: 0.6662 (tp) REVERT: B 311 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7509 (tp) REVERT: B 334 MET cc_start: 0.3941 (OUTLIER) cc_final: 0.2022 (mtt) REVERT: C 67 MET cc_start: 0.7217 (mmm) cc_final: 0.6847 (ttt) REVERT: C 159 ASN cc_start: 0.8219 (m-40) cc_final: 0.7785 (m-40) REVERT: C 219 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7335 (mmpt) REVERT: C 300 LEU cc_start: 0.7438 (mt) cc_final: 0.6683 (tp) REVERT: C 311 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7511 (tp) REVERT: C 334 MET cc_start: 0.3965 (OUTLIER) cc_final: 0.2010 (mtt) REVERT: D 159 ASN cc_start: 0.8225 (m-40) cc_final: 0.7792 (m-40) REVERT: D 219 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7360 (mmpt) REVERT: D 245 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6778 (mp) REVERT: D 300 LEU cc_start: 0.7467 (mt) cc_final: 0.6697 (tp) REVERT: D 311 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7515 (tp) REVERT: D 334 MET cc_start: 0.4012 (OUTLIER) cc_final: 0.2115 (mtt) outliers start: 50 outliers final: 17 residues processed: 201 average time/residue: 0.6145 time to fit residues: 135.7267 Evaluate side-chains 205 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 518 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 79 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 0.0050 chunk 171 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS D 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107331 restraints weight = 15826.284| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.96 r_work: 0.3136 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14400 Z= 0.122 Angle : 0.477 5.304 19560 Z= 0.265 Chirality : 0.039 0.126 2268 Planarity : 0.004 0.044 2412 Dihedral : 4.250 19.822 1904 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.12 % Allowed : 16.65 % Favored : 81.23 % 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 aren not related in a simple way. whole: 2.21 (0.21), residues: 1724 helix: 2.95 (0.16), residues: 1016 sheet: 1.09 (0.36), residues: 196 loop : -1.66 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.013 0.001 TYR D 497 PHE 0.011 0.001 PHE B 474 TRP 0.007 0.001 TRP C 398 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00247 (14392) covalent geometry : angle 0.47582 (19544) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.05774 ( 16) hydrogen bonds : bond 0.05075 ( 992) hydrogen bonds : angle 3.97075 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8169 (m-40) cc_final: 0.7772 (m-40) REVERT: A 300 LEU cc_start: 0.7480 (mt) cc_final: 0.6709 (tp) REVERT: A 419 ARG cc_start: 0.7406 (ttp-110) cc_final: 0.6866 (ttm170) REVERT: B 67 MET cc_start: 0.7061 (mmm) cc_final: 0.6701 (ttt) REVERT: B 159 ASN cc_start: 0.8208 (m-40) cc_final: 0.7774 (m-40) REVERT: B 219 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7297 (mmpt) REVERT: B 300 LEU cc_start: 0.7375 (mt) cc_final: 0.6595 (tp) REVERT: B 311 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7523 (tp) REVERT: C 67 MET cc_start: 0.7033 (mmm) cc_final: 0.6691 (ttt) REVERT: C 159 ASN cc_start: 0.8203 (m-40) cc_final: 0.7773 (m-40) REVERT: C 219 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7295 (mmpt) REVERT: C 300 LEU cc_start: 0.7379 (mt) cc_final: 0.6594 (tp) REVERT: C 311 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7532 (tp) REVERT: D 159 ASN cc_start: 0.8188 (m-40) cc_final: 0.7758 (m-40) REVERT: D 219 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7314 (mmpt) REVERT: D 300 LEU cc_start: 0.7394 (mt) cc_final: 0.6608 (tp) REVERT: D 311 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7538 (tp) outliers start: 33 outliers final: 13 residues processed: 207 average time/residue: 0.5885 time to fit residues: 134.3313 Evaluate side-chains 204 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 359 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 135 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 69 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100102 restraints weight = 15800.699| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.99 r_work: 0.3025 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14400 Z= 0.206 Angle : 0.586 6.518 19560 Z= 0.324 Chirality : 0.043 0.149 2268 Planarity : 0.004 0.041 2412 Dihedral : 4.604 23.832 1904 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.70 % Allowed : 15.49 % Favored : 81.81 % 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 aren not related in a simple way. whole: 1.80 (0.20), residues: 1724 helix: 2.59 (0.16), residues: 1016 sheet: 0.05 (0.32), residues: 252 loop : -1.46 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 419 TYR 0.013 0.001 TYR B 497 PHE 0.013 0.002 PHE C 505 TRP 0.012 0.002 TRP C 398 HIS 0.003 0.001 HIS D 234 Details of bonding type rmsd covalent geometry : bond 0.00480 (14392) covalent geometry : angle 0.58451 (19544) SS BOND : bond 0.00424 ( 8) SS BOND : angle 1.41332 ( 16) hydrogen bonds : bond 0.06935 ( 992) hydrogen bonds : angle 4.33287 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8230 (m-40) cc_final: 0.7825 (m-40) REVERT: A 182 PHE cc_start: 0.8655 (p90) cc_final: 0.8406 (p90) REVERT: A 300 LEU cc_start: 0.7665 (mt) cc_final: 0.6890 (tp) REVERT: A 419 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.6940 (ttm170) REVERT: B 67 MET cc_start: 0.7240 (mmm) cc_final: 0.6894 (ttt) REVERT: B 159 ASN cc_start: 0.8274 (m-40) cc_final: 0.7838 (m-40) REVERT: B 219 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7419 (mmpt) REVERT: B 300 LEU cc_start: 0.7499 (mt) cc_final: 0.6749 (tp) REVERT: B 311 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7615 (tp) REVERT: B 376 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: C 67 MET cc_start: 0.7239 (mmm) cc_final: 0.6886 (ttt) REVERT: C 159 ASN cc_start: 0.8263 (m-40) cc_final: 0.7827 (m-40) REVERT: C 219 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7410 (mmpt) REVERT: C 300 LEU cc_start: 0.7503 (mt) cc_final: 0.6755 (tp) REVERT: C 311 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7625 (tp) REVERT: C 376 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: D 159 ASN cc_start: 0.8252 (m-40) cc_final: 0.7819 (m-40) REVERT: D 219 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7436 (mmpt) REVERT: D 245 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6893 (mp) REVERT: D 300 LEU cc_start: 0.7537 (mt) cc_final: 0.6777 (tp) REVERT: D 311 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7619 (tp) REVERT: D 376 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7480 (mt-10) outliers start: 42 outliers final: 18 residues processed: 199 average time/residue: 0.6088 time to fit residues: 132.7424 Evaluate side-chains 196 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 518 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104106 restraints weight = 15836.103| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.97 r_work: 0.3084 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14400 Z= 0.140 Angle : 0.511 5.663 19560 Z= 0.284 Chirality : 0.040 0.129 2268 Planarity : 0.004 0.041 2412 Dihedral : 4.416 23.643 1904 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.19 % Allowed : 16.65 % Favored : 81.17 % 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 aren not related in a simple way. whole: 2.00 (0.21), residues: 1724 helix: 2.80 (0.16), residues: 1016 sheet: 0.10 (0.32), residues: 252 loop : -1.50 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 419 TYR 0.014 0.001 TYR B 497 PHE 0.011 0.001 PHE B 474 TRP 0.008 0.001 TRP B 398 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00297 (14392) covalent geometry : angle 0.51026 (19544) SS BOND : bond 0.00312 ( 8) SS BOND : angle 1.10851 ( 16) hydrogen bonds : bond 0.05717 ( 992) hydrogen bonds : angle 4.10778 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8193 (m-40) cc_final: 0.7783 (m-40) REVERT: A 182 PHE cc_start: 0.8624 (p90) cc_final: 0.8375 (p90) REVERT: A 300 LEU cc_start: 0.7498 (mt) cc_final: 0.6741 (tp) REVERT: A 376 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: A 419 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6883 (ttm170) REVERT: B 67 MET cc_start: 0.7104 (mmm) cc_final: 0.6771 (ttt) REVERT: B 159 ASN cc_start: 0.8261 (m-40) cc_final: 0.7827 (m-40) REVERT: B 219 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7309 (mmpt) REVERT: B 300 LEU cc_start: 0.7403 (mt) cc_final: 0.6648 (tp) REVERT: B 311 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7557 (tp) REVERT: C 67 MET cc_start: 0.7126 (mmm) cc_final: 0.6773 (ttt) REVERT: C 159 ASN cc_start: 0.8241 (m-40) cc_final: 0.7808 (m-40) REVERT: C 219 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7313 (mmpt) REVERT: C 300 LEU cc_start: 0.7388 (mt) cc_final: 0.6638 (tp) REVERT: C 311 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7574 (tp) REVERT: D 159 ASN cc_start: 0.8264 (m-40) cc_final: 0.7834 (m-40) REVERT: D 219 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7332 (mmpt) REVERT: D 300 LEU cc_start: 0.7413 (mt) cc_final: 0.6642 (tp) REVERT: D 311 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7568 (tp) outliers start: 34 outliers final: 18 residues processed: 194 average time/residue: 0.5578 time to fit residues: 119.2665 Evaluate side-chains 196 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105713 restraints weight = 15917.603| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.98 r_work: 0.3110 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14400 Z= 0.130 Angle : 0.499 5.649 19560 Z= 0.277 Chirality : 0.039 0.127 2268 Planarity : 0.004 0.042 2412 Dihedral : 4.312 23.978 1904 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.80 % Allowed : 16.77 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.21), residues: 1724 helix: 2.90 (0.16), residues: 1016 sheet: 0.96 (0.35), residues: 204 loop : -1.69 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.014 0.001 TYR C 497 PHE 0.012 0.001 PHE D 474 TRP 0.008 0.001 TRP C 398 HIS 0.003 0.000 HIS D 234 Details of bonding type rmsd covalent geometry : bond 0.00268 (14392) covalent geometry : angle 0.49778 (19544) SS BOND : bond 0.00272 ( 8) SS BOND : angle 1.06430 ( 16) hydrogen bonds : bond 0.05375 ( 992) hydrogen bonds : angle 4.02468 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8185 (m-40) cc_final: 0.7769 (m-40) REVERT: A 300 LEU cc_start: 0.7486 (mt) cc_final: 0.6735 (tp) REVERT: A 376 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: A 419 ARG cc_start: 0.7395 (ttp-110) cc_final: 0.6859 (ttm170) REVERT: B 67 MET cc_start: 0.7057 (mmm) cc_final: 0.6699 (ttt) REVERT: B 159 ASN cc_start: 0.8250 (m-40) cc_final: 0.7804 (m-40) REVERT: B 219 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7303 (mmpt) REVERT: B 300 LEU cc_start: 0.7409 (mt) cc_final: 0.6639 (tp) REVERT: B 311 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7506 (tp) REVERT: B 383 TYR cc_start: 0.7814 (m-80) cc_final: 0.7593 (m-80) REVERT: C 67 MET cc_start: 0.7078 (mmm) cc_final: 0.6712 (ttt) REVERT: C 159 ASN cc_start: 0.8244 (m-40) cc_final: 0.7799 (m-40) REVERT: C 219 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7318 (mmpt) REVERT: C 300 LEU cc_start: 0.7414 (mt) cc_final: 0.6638 (tp) REVERT: C 311 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7535 (tp) REVERT: C 383 TYR cc_start: 0.7812 (m-80) cc_final: 0.7578 (m-80) REVERT: D 159 ASN cc_start: 0.8258 (m-40) cc_final: 0.7830 (m-40) REVERT: D 219 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7329 (mmpt) REVERT: D 300 LEU cc_start: 0.7418 (mt) cc_final: 0.6637 (tp) REVERT: D 311 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7526 (tp) outliers start: 28 outliers final: 17 residues processed: 186 average time/residue: 0.6179 time to fit residues: 126.2787 Evaluate side-chains 197 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103940 restraints weight = 15784.281| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.99 r_work: 0.3083 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14400 Z= 0.144 Angle : 0.514 5.811 19560 Z= 0.286 Chirality : 0.040 0.128 2268 Planarity : 0.004 0.040 2412 Dihedral : 4.372 21.512 1904 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.25 % Allowed : 16.45 % Favored : 81.30 % 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 aren not related in a simple way. whole: 2.01 (0.21), residues: 1724 helix: 2.83 (0.16), residues: 1016 sheet: -0.01 (0.32), residues: 260 loop : -1.49 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.014 0.001 TYR C 497 PHE 0.012 0.001 PHE B 474 TRP 0.010 0.001 TRP C 398 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00309 (14392) covalent geometry : angle 0.51358 (19544) SS BOND : bond 0.00300 ( 8) SS BOND : angle 1.12737 ( 16) hydrogen bonds : bond 0.05754 ( 992) hydrogen bonds : angle 4.09833 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5956.82 seconds wall clock time: 102 minutes 9.78 seconds (6129.78 seconds total)