Starting phenix.real_space_refine on Tue Aug 26 16:01:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1h_35922/08_2025/8j1h_35922_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1h_35922/08_2025/8j1h_35922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1h_35922/08_2025/8j1h_35922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1h_35922/08_2025/8j1h_35922.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1h_35922/08_2025/8j1h_35922_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1h_35922/08_2025/8j1h_35922_trim.cif" } resolution = 3.88 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 96 5.16 5 C 12480 2.51 5 N 3168 2.21 5 O 3388 1.98 5 F 8 1.80 5 H 19324 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38464 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B, A Time building chain proxies: 11.18, per 1000 atoms: 0.29 Number of scatterers: 38464 At special positions: 0 Unit cell: (160.89, 160.89, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 F 8 9.00 O 3388 8.00 N 3168 7.00 C 12480 6.00 H 19324 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 924.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 65.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.509A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 4.200A pdb=" N GLY C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.885A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.582A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.648A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 322 through 331 removed outlier: 3.689A pdb=" N HIS C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 357 removed outlier: 3.801A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 5.499A pdb=" N HIS C 401 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 402 " --> pdb=" O THR C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.058A pdb=" N MET C 449 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 450' Processing helix chain 'C' and resid 453 through 467 removed outlier: 3.672A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 490 Processing helix chain 'C' and resid 504 through 531 Processing helix chain 'C' and resid 550 through 570 removed outlier: 3.711A pdb=" N ALA C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 593 removed outlier: 3.763A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 610 Processing helix chain 'C' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 677 Processing helix chain 'C' and resid 696 through 724 removed outlier: 3.816A pdb=" N THR C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 748 removed outlier: 3.699A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.509A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 4.199A pdb=" N GLY D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.884A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.583A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.647A pdb=" N GLN D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 322 through 331 removed outlier: 3.689A pdb=" N HIS D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 357 removed outlier: 3.800A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 403 removed outlier: 5.500A pdb=" N HIS D 401 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 402 " --> pdb=" O THR D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 450 removed outlier: 4.057A pdb=" N MET D 449 " --> pdb=" O ASN D 445 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 445 through 450' Processing helix chain 'D' and resid 453 through 467 removed outlier: 3.673A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 490 Processing helix chain 'D' and resid 504 through 531 Processing helix chain 'D' and resid 550 through 570 removed outlier: 3.711A pdb=" N ALA D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 593 removed outlier: 3.764A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 610 Processing helix chain 'D' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 677 Processing helix chain 'D' and resid 696 through 724 removed outlier: 3.816A pdb=" N THR D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 748 removed outlier: 3.698A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.508A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 4.200A pdb=" N GLY B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.884A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.581A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.648A pdb=" N GLN B 274 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.689A pdb=" N HIS B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.801A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 5.499A pdb=" N HIS B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.057A pdb=" N MET B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 450' Processing helix chain 'B' and resid 453 through 467 removed outlier: 3.673A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 490 Processing helix chain 'B' and resid 504 through 531 Processing helix chain 'B' and resid 550 through 570 removed outlier: 3.712A pdb=" N ALA B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 593 removed outlier: 3.764A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 696 through 724 removed outlier: 3.817A pdb=" N THR B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 748 removed outlier: 3.699A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.508A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 4.200A pdb=" N GLY A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.884A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.582A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.649A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.688A pdb=" N HIS A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.801A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 390 removed outlier: 4.095A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 5.499A pdb=" N HIS A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.057A pdb=" N MET A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.673A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 490 Processing helix chain 'A' and resid 504 through 531 Processing helix chain 'A' and resid 550 through 570 removed outlier: 3.712A pdb=" N ALA A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 593 removed outlier: 3.763A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.798A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 696 through 724 removed outlier: 3.816A pdb=" N THR A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 748 removed outlier: 3.698A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 407 through 410 removed outlier: 3.942A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 407 through 410 removed outlier: 3.942A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 407 through 410 removed outlier: 3.942A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 410 removed outlier: 3.943A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2928 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: 7.31 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19292 1.03 - 1.23: 54 1.23 - 1.42: 8234 1.42 - 1.62: 11160 1.62 - 1.82: 160 Bond restraints: 38900 Sorted by residual: bond pdb=" C7 9QM D 901 " pdb=" O1 9QM D 901 " ideal model delta sigma weight residual 1.213 1.398 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C7 9QM B 901 " pdb=" O1 9QM B 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" C7 9QM A 901 " pdb=" O1 9QM A 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C7 9QM C 901 " pdb=" O1 9QM C 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C23 9QM B 901 " pdb=" C25 9QM B 901 " ideal model delta sigma weight residual 1.382 1.526 -0.144 2.00e-02 2.50e+03 5.15e+01 ... (remaining 38895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 70164 7.50 - 15.00: 16 15.00 - 22.49: 0 22.49 - 29.99: 16 29.99 - 37.49: 20 Bond angle restraints: 70216 Sorted by residual: angle pdb=" C SER D 688 " pdb=" CA SER D 688 " pdb=" HA SER D 688 " ideal model delta sigma weight residual 109.00 71.51 37.49 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER C 688 " pdb=" CA SER C 688 " pdb=" HA SER C 688 " ideal model delta sigma weight residual 109.00 71.51 37.49 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER A 688 " pdb=" CA SER A 688 " pdb=" HA SER A 688 " ideal model delta sigma weight residual 109.00 71.53 37.47 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER B 688 " pdb=" CA SER B 688 " pdb=" HA SER B 688 " ideal model delta sigma weight residual 109.00 71.55 37.45 3.00e+00 1.11e-01 1.56e+02 angle pdb=" N ILE C 696 " pdb=" CA ILE C 696 " pdb=" HA ILE C 696 " ideal model delta sigma weight residual 110.00 73.76 36.24 3.00e+00 1.11e-01 1.46e+02 ... (remaining 70211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16306 17.76 - 35.53: 1445 35.53 - 53.29: 377 53.29 - 71.06: 84 71.06 - 88.82: 16 Dihedral angle restraints: 18228 sinusoidal: 9836 harmonic: 8392 Sorted by residual: dihedral pdb=" CA LYS C 727 " pdb=" C LYS C 727 " pdb=" N GLU C 728 " pdb=" CA GLU C 728 " ideal model delta harmonic sigma weight residual 180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS B 727 " pdb=" C LYS B 727 " pdb=" N GLU B 728 " pdb=" CA GLU B 728 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LYS A 727 " pdb=" C LYS A 727 " pdb=" N GLU A 728 " pdb=" CA GLU A 728 " ideal model delta harmonic sigma weight residual 180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 18225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 3020 0.276 - 0.552: 8 0.552 - 0.829: 0 0.829 - 1.105: 0 1.105 - 1.381: 4 Chirality restraints: 3032 Sorted by residual: chirality pdb=" CB THR B 701 " pdb=" CA THR B 701 " pdb=" OG1 THR B 701 " pdb=" CG2 THR B 701 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.77e+01 chirality pdb=" CB THR A 701 " pdb=" CA THR A 701 " pdb=" OG1 THR A 701 " pdb=" CG2 THR A 701 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" CB THR C 701 " pdb=" CA THR C 701 " pdb=" OG1 THR C 701 " pdb=" CG2 THR C 701 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.38 2.00e-01 2.50e+01 4.73e+01 ... (remaining 3029 not shown) Planarity restraints: 5540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 737 " 0.024 2.00e-02 2.50e+03 1.40e-02 7.86e+00 pdb=" CG TRP C 737 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP C 737 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 737 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 737 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 737 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 737 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 737 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 737 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 737 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP C 737 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP C 737 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP C 737 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 737 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 737 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP C 737 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 737 " -0.024 2.00e-02 2.50e+03 1.40e-02 7.82e+00 pdb=" CG TRP A 737 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 737 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 737 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 737 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 737 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 737 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 737 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 737 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 737 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 737 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 737 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 737 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 737 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 737 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 737 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 737 " -0.024 2.00e-02 2.50e+03 1.40e-02 7.80e+00 pdb=" CG TRP D 737 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP D 737 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 737 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 737 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 737 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 737 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 737 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 737 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 737 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP D 737 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP D 737 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP D 737 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 737 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 737 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP D 737 " -0.001 2.00e-02 2.50e+03 ... (remaining 5537 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1800 2.14 - 2.76: 76208 2.76 - 3.37: 113496 3.37 - 3.99: 137626 3.99 - 4.60: 213897 Nonbonded interactions: 543027 Sorted by model distance: nonbonded pdb="HD22 ASN D 474 " pdb=" O1 9QM D 901 " model vdw 1.525 2.450 nonbonded pdb="HD22 ASN A 474 " pdb=" O1 9QM A 901 " model vdw 1.525 2.450 nonbonded pdb="HD22 ASN B 474 " pdb=" O1 9QM B 901 " model vdw 1.525 2.450 nonbonded pdb="HD22 ASN C 474 " pdb=" O1 9QM C 901 " model vdw 1.526 2.450 nonbonded pdb=" OD1 ASP B 318 " pdb=" H ASN B 322 " model vdw 1.543 2.450 ... (remaining 543022 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.460 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.900 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 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 : 0.009 0.185 19576 Z= 0.414 Angle : 0.757 11.030 26524 Z= 0.414 Chirality : 0.067 1.381 3032 Planarity : 0.004 0.036 3280 Dihedral : 13.707 73.260 7148 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.00 % Favored : 87.48 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % 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: -1.29 (0.18), residues: 2316 helix: 0.33 (0.15), residues: 1264 sheet: -0.17 (0.67), residues: 64 loop : -2.57 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 404 TYR 0.034 0.002 TYR C 346 PHE 0.036 0.002 PHE B 524 TRP 0.047 0.003 TRP C 737 HIS 0.003 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00851 (19576) covalent geometry : angle 0.75680 (26524) hydrogen bonds : bond 0.15368 ( 1012) hydrogen bonds : angle 6.32840 ( 2928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 318 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 271 ARG cc_start: 0.7609 (tpm170) cc_final: 0.7168 (tpp-160) REVERT: D 271 ARG cc_start: 0.7558 (tpm170) cc_final: 0.7113 (tpp-160) REVERT: B 271 ARG cc_start: 0.7727 (tpm170) cc_final: 0.7288 (tpp-160) REVERT: A 271 ARG cc_start: 0.7641 (tpm170) cc_final: 0.7169 (tpp-160) REVERT: A 578 MET cc_start: 0.7695 (tmm) cc_final: 0.7424 (tmm) REVERT: A 742 LEU cc_start: 0.8528 (mm) cc_final: 0.8157 (tp) outliers start: 4 outliers final: 3 residues processed: 318 average time/residue: 0.2797 time to fit residues: 137.6892 Evaluate side-chains 265 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 262 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 GLN D 267 GLN B 267 GLN A 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.167841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.132492 restraints weight = 143163.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.138247 restraints weight = 73194.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.141833 restraints weight = 48996.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.144137 restraints weight = 38346.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.145501 restraints weight = 32759.431| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19576 Z= 0.201 Angle : 0.718 11.133 26524 Z= 0.389 Chirality : 0.068 1.446 3032 Planarity : 0.006 0.075 3280 Dihedral : 5.530 59.136 2669 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.18 % Favored : 88.47 % Rotamer: Outliers : 1.15 % Allowed : 7.39 % Favored : 91.46 % 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: -1.57 (0.17), residues: 2316 helix: 0.05 (0.14), residues: 1300 sheet: -0.08 (0.67), residues: 64 loop : -2.73 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 757 TYR 0.022 0.002 TYR B 553 PHE 0.021 0.002 PHE B 524 TRP 0.030 0.002 TRP A 737 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00440 (19576) covalent geometry : angle 0.71814 (26524) hydrogen bonds : bond 0.05047 ( 1012) hydrogen bonds : angle 5.60686 ( 2928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 346 TYR cc_start: 0.8296 (t80) cc_final: 0.8088 (t80) REVERT: D 346 TYR cc_start: 0.8277 (t80) cc_final: 0.8069 (t80) REVERT: B 223 MET cc_start: 0.6931 (ppp) cc_final: 0.6690 (mmm) REVERT: B 346 TYR cc_start: 0.8334 (t80) cc_final: 0.8096 (t80) REVERT: B 482 MET cc_start: 0.6581 (mmp) cc_final: 0.6297 (mmt) REVERT: A 578 MET cc_start: 0.7652 (tmm) cc_final: 0.7428 (tmm) REVERT: A 742 LEU cc_start: 0.8531 (mm) cc_final: 0.8226 (tp) outliers start: 24 outliers final: 21 residues processed: 295 average time/residue: 0.2970 time to fit residues: 134.6431 Evaluate side-chains 296 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 275 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 224 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 188 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.0870 chunk 229 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.168573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.133622 restraints weight = 142201.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.139409 restraints weight = 72466.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.143071 restraints weight = 48295.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.145443 restraints weight = 37503.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.146888 restraints weight = 31888.969| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19576 Z= 0.157 Angle : 0.676 11.276 26524 Z= 0.360 Chirality : 0.067 1.434 3032 Planarity : 0.005 0.084 3280 Dihedral : 5.207 55.032 2666 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.31 % Favored : 88.34 % Rotamer: Outliers : 1.20 % Allowed : 9.64 % Favored : 89.16 % 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: -1.40 (0.17), residues: 2316 helix: 0.26 (0.14), residues: 1304 sheet: 0.18 (0.68), residues: 64 loop : -2.79 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 757 TYR 0.018 0.001 TYR A 628 PHE 0.020 0.001 PHE B 524 TRP 0.023 0.001 TRP C 737 HIS 0.002 0.000 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00348 (19576) covalent geometry : angle 0.67596 (26524) hydrogen bonds : bond 0.04498 ( 1012) hydrogen bonds : angle 5.38857 ( 2928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 TYR cc_start: 0.8302 (t80) cc_final: 0.7630 (t80) REVERT: A 482 MET cc_start: 0.6450 (mmp) cc_final: 0.6029 (mmp) outliers start: 25 outliers final: 18 residues processed: 283 average time/residue: 0.3201 time to fit residues: 137.6502 Evaluate side-chains 284 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 266 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 34 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 209 optimal weight: 0.0770 chunk 118 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 173 optimal weight: 0.1980 chunk 50 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 302 ASN A 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.167707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.132473 restraints weight = 142834.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.138179 restraints weight = 73306.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.141807 restraints weight = 49031.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.144079 restraints weight = 38250.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.145519 restraints weight = 32673.035| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19576 Z= 0.187 Angle : 0.679 11.206 26524 Z= 0.364 Chirality : 0.067 1.435 3032 Planarity : 0.005 0.047 3280 Dihedral : 5.064 52.584 2663 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.52 % Favored : 87.13 % Rotamer: Outliers : 1.30 % Allowed : 12.00 % Favored : 86.71 % 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: -1.39 (0.17), residues: 2316 helix: 0.27 (0.14), residues: 1316 sheet: 0.17 (0.68), residues: 64 loop : -2.83 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 271 TYR 0.019 0.002 TYR D 553 PHE 0.018 0.001 PHE B 524 TRP 0.020 0.001 TRP C 737 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00406 (19576) covalent geometry : angle 0.67901 (26524) hydrogen bonds : bond 0.04351 ( 1012) hydrogen bonds : angle 5.35555 ( 2928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6338 (mmp) cc_final: 0.6084 (mmp) REVERT: B 287 LEU cc_start: 0.9053 (mp) cc_final: 0.8685 (mp) REVERT: B 482 MET cc_start: 0.6649 (mmp) cc_final: 0.6325 (mmt) REVERT: A 482 MET cc_start: 0.6517 (mmp) cc_final: 0.5861 (mmp) outliers start: 27 outliers final: 21 residues processed: 284 average time/residue: 0.2913 time to fit residues: 127.1368 Evaluate side-chains 286 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 161 optimal weight: 0.7980 chunk 93 optimal weight: 0.0870 chunk 70 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 225 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.169507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.134862 restraints weight = 142490.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.140567 restraints weight = 74130.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.144201 restraints weight = 49917.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.146493 restraints weight = 38937.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.147906 restraints weight = 33245.960| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19576 Z= 0.138 Angle : 0.653 11.353 26524 Z= 0.346 Chirality : 0.066 1.435 3032 Planarity : 0.004 0.039 3280 Dihedral : 4.901 49.037 2663 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.61 % Favored : 88.04 % Rotamer: Outliers : 1.25 % Allowed : 12.14 % Favored : 86.61 % 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: -1.16 (0.17), residues: 2316 helix: 0.47 (0.14), residues: 1312 sheet: 0.41 (0.69), residues: 64 loop : -2.76 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.028 0.001 TYR B 553 PHE 0.028 0.001 PHE B 524 TRP 0.019 0.001 TRP C 737 HIS 0.002 0.000 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00303 (19576) covalent geometry : angle 0.65320 (26524) hydrogen bonds : bond 0.04135 ( 1012) hydrogen bonds : angle 5.17768 ( 2928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 482 MET cc_start: 0.6533 (mmp) cc_final: 0.6036 (mmp) REVERT: B 287 LEU cc_start: 0.8989 (mp) cc_final: 0.8613 (mp) REVERT: A 482 MET cc_start: 0.6486 (mmp) cc_final: 0.6006 (mmp) outliers start: 26 outliers final: 20 residues processed: 289 average time/residue: 0.3363 time to fit residues: 146.7839 Evaluate side-chains 284 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 156 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.169057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.134333 restraints weight = 143354.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.140164 restraints weight = 72711.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.143858 restraints weight = 48241.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.146129 restraints weight = 37366.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.147496 restraints weight = 31848.431| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19576 Z= 0.143 Angle : 0.648 11.425 26524 Z= 0.345 Chirality : 0.066 1.447 3032 Planarity : 0.005 0.098 3280 Dihedral : 4.971 46.070 2663 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.66 % Favored : 88.00 % Rotamer: Outliers : 1.54 % Allowed : 13.29 % Favored : 85.17 % 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: -1.10 (0.17), residues: 2316 helix: 0.56 (0.14), residues: 1308 sheet: 0.54 (0.71), residues: 64 loop : -2.79 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 757 TYR 0.024 0.001 TYR D 553 PHE 0.026 0.001 PHE B 524 TRP 0.018 0.001 TRP D 737 HIS 0.005 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00314 (19576) covalent geometry : angle 0.64804 (26524) hydrogen bonds : bond 0.04030 ( 1012) hydrogen bonds : angle 5.12080 ( 2928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 482 MET cc_start: 0.6482 (mmp) cc_final: 0.5957 (mmp) REVERT: B 287 LEU cc_start: 0.8984 (mp) cc_final: 0.8600 (mp) REVERT: A 482 MET cc_start: 0.6448 (mmp) cc_final: 0.5973 (mmp) outliers start: 32 outliers final: 24 residues processed: 283 average time/residue: 0.3531 time to fit residues: 151.9522 Evaluate side-chains 286 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 715 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 223 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 217 optimal weight: 30.0000 chunk 206 optimal weight: 0.8980 chunk 151 optimal weight: 0.0000 chunk 227 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.170431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.136098 restraints weight = 143510.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.141875 restraints weight = 73901.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.145484 restraints weight = 49409.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.147756 restraints weight = 38444.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.148922 restraints weight = 32783.108| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19576 Z= 0.131 Angle : 0.645 11.469 26524 Z= 0.342 Chirality : 0.066 1.455 3032 Planarity : 0.005 0.070 3280 Dihedral : 4.876 31.433 2660 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.32 % Favored : 89.34 % Rotamer: Outliers : 1.58 % Allowed : 13.39 % Favored : 85.03 % 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: -0.99 (0.17), residues: 2316 helix: 0.75 (0.14), residues: 1284 sheet: 0.60 (0.72), residues: 64 loop : -2.82 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 269 TYR 0.028 0.001 TYR C 553 PHE 0.032 0.001 PHE D 524 TRP 0.018 0.001 TRP A 737 HIS 0.002 0.000 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00286 (19576) covalent geometry : angle 0.64497 (26524) hydrogen bonds : bond 0.03952 ( 1012) hydrogen bonds : angle 5.02554 ( 2928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6317 (mmp) cc_final: 0.5870 (mmp) REVERT: D 287 LEU cc_start: 0.8917 (mp) cc_final: 0.8579 (mp) REVERT: D 482 MET cc_start: 0.6499 (mmp) cc_final: 0.5966 (mmp) REVERT: B 287 LEU cc_start: 0.8983 (mp) cc_final: 0.8624 (mp) REVERT: A 287 LEU cc_start: 0.8935 (mp) cc_final: 0.8582 (mp) REVERT: A 482 MET cc_start: 0.6483 (mmp) cc_final: 0.5989 (mmp) outliers start: 33 outliers final: 22 residues processed: 287 average time/residue: 0.3186 time to fit residues: 138.4133 Evaluate side-chains 281 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 715 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 215 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 67 optimal weight: 0.0770 chunk 70 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 209 optimal weight: 0.0570 chunk 115 optimal weight: 6.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.170970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136754 restraints weight = 142232.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.142749 restraints weight = 70120.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.146485 restraints weight = 45844.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.148839 restraints weight = 35274.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.150330 restraints weight = 29850.553| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19576 Z= 0.120 Angle : 0.641 11.473 26524 Z= 0.338 Chirality : 0.066 1.447 3032 Planarity : 0.004 0.043 3280 Dihedral : 4.610 24.827 2660 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.45 % Favored : 89.21 % Rotamer: Outliers : 1.10 % Allowed : 14.44 % Favored : 84.45 % 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: -0.79 (0.18), residues: 2316 helix: 0.93 (0.14), residues: 1288 sheet: 0.68 (0.73), residues: 64 loop : -2.78 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 757 TYR 0.023 0.001 TYR A 553 PHE 0.028 0.001 PHE C 524 TRP 0.020 0.001 TRP A 737 HIS 0.005 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00258 (19576) covalent geometry : angle 0.64109 (26524) hydrogen bonds : bond 0.03778 ( 1012) hydrogen bonds : angle 4.89250 ( 2928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 LEU cc_start: 0.8852 (mp) cc_final: 0.8530 (mp) REVERT: C 482 MET cc_start: 0.6221 (mmp) cc_final: 0.5766 (mmp) REVERT: D 287 LEU cc_start: 0.8847 (mp) cc_final: 0.8538 (mp) REVERT: D 334 ASN cc_start: 0.7072 (p0) cc_final: 0.6508 (t0) REVERT: D 482 MET cc_start: 0.6398 (mmp) cc_final: 0.5865 (mmp) REVERT: B 287 LEU cc_start: 0.8947 (mp) cc_final: 0.8605 (mp) REVERT: B 713 MET cc_start: 0.8366 (ppp) cc_final: 0.8111 (tmm) REVERT: A 287 LEU cc_start: 0.8888 (mp) cc_final: 0.8567 (mp) REVERT: A 482 MET cc_start: 0.6449 (mmp) cc_final: 0.5979 (mmp) outliers start: 23 outliers final: 20 residues processed: 275 average time/residue: 0.3248 time to fit residues: 134.7357 Evaluate side-chains 279 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.167089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.136538 restraints weight = 145018.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137471 restraints weight = 73109.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.139079 restraints weight = 60376.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139441 restraints weight = 51224.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.140670 restraints weight = 47752.249| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19576 Z= 0.240 Angle : 0.714 11.369 26524 Z= 0.387 Chirality : 0.068 1.459 3032 Planarity : 0.005 0.048 3280 Dihedral : 4.985 24.666 2660 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.00 % Favored : 87.65 % Rotamer: Outliers : 1.44 % Allowed : 14.97 % Favored : 83.59 % 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: -1.15 (0.17), residues: 2316 helix: 0.58 (0.14), residues: 1296 sheet: 0.92 (0.76), residues: 64 loop : -2.90 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 269 TYR 0.022 0.002 TYR A 556 PHE 0.058 0.002 PHE D 524 TRP 0.017 0.002 TRP A 737 HIS 0.006 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00518 (19576) covalent geometry : angle 0.71442 (26524) hydrogen bonds : bond 0.04210 ( 1012) hydrogen bonds : angle 5.20670 ( 2928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 TYR cc_start: 0.8446 (t80) cc_final: 0.8238 (t80) REVERT: D 482 MET cc_start: 0.6894 (mmp) cc_final: 0.6258 (mmp) REVERT: B 713 MET cc_start: 0.8543 (ppp) cc_final: 0.8315 (tmm) REVERT: A 482 MET cc_start: 0.6913 (mmp) cc_final: 0.6304 (mmp) outliers start: 30 outliers final: 29 residues processed: 283 average time/residue: 0.3326 time to fit residues: 144.1800 Evaluate side-chains 295 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 715 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 0.0020 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.170038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.136589 restraints weight = 141016.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.142236 restraints weight = 72592.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.145850 restraints weight = 48504.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.148114 restraints weight = 37596.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.149559 restraints weight = 31904.973| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19576 Z= 0.125 Angle : 0.665 11.467 26524 Z= 0.349 Chirality : 0.066 1.443 3032 Planarity : 0.004 0.046 3280 Dihedral : 4.726 24.999 2660 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.84 % Favored : 89.81 % Rotamer: Outliers : 1.01 % Allowed : 15.55 % Favored : 83.45 % 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: -0.84 (0.18), residues: 2316 helix: 0.86 (0.14), residues: 1292 sheet: 0.72 (0.73), residues: 64 loop : -2.78 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 269 TYR 0.029 0.001 TYR A 553 PHE 0.053 0.001 PHE C 524 TRP 0.018 0.001 TRP A 737 HIS 0.004 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00276 (19576) covalent geometry : angle 0.66489 (26524) hydrogen bonds : bond 0.03815 ( 1012) hydrogen bonds : angle 4.94603 ( 2928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6338 (mmp) cc_final: 0.5870 (mmp) REVERT: D 482 MET cc_start: 0.6498 (mmp) cc_final: 0.5968 (mmp) REVERT: B 713 MET cc_start: 0.8416 (ppp) cc_final: 0.8121 (tmm) REVERT: A 482 MET cc_start: 0.6538 (mmp) cc_final: 0.6049 (mmp) outliers start: 21 outliers final: 18 residues processed: 278 average time/residue: 0.3647 time to fit residues: 155.4327 Evaluate side-chains 277 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 715 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 144 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 198 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.171100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136824 restraints weight = 144514.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.142644 restraints weight = 74877.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.146269 restraints weight = 50187.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.148536 restraints weight = 39118.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.149987 restraints weight = 33319.575| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19576 Z= 0.127 Angle : 0.659 11.405 26524 Z= 0.346 Chirality : 0.066 1.435 3032 Planarity : 0.004 0.048 3280 Dihedral : 4.745 25.084 2660 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.32 % Favored : 89.34 % Rotamer: Outliers : 1.06 % Allowed : 15.55 % Favored : 83.40 % 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: -0.80 (0.18), residues: 2316 helix: 0.88 (0.14), residues: 1304 sheet: 0.76 (0.75), residues: 64 loop : -2.77 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 269 TYR 0.017 0.001 TYR B 553 PHE 0.070 0.001 PHE C 524 TRP 0.019 0.001 TRP A 737 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00283 (19576) covalent geometry : angle 0.65915 (26524) hydrogen bonds : bond 0.03791 ( 1012) hydrogen bonds : angle 4.91159 ( 2928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6427.54 seconds wall clock time: 110 minutes 30.91 seconds (6630.91 seconds total)