Starting phenix.real_space_refine on Fri Jul 3 14:54:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rhk_24464/07_2026/7rhk_24464.cif" } resolution = 3.27 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= 0.005 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 83 5.16 5 C 9581 2.51 5 N 2389 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14682 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3438 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 14, 'TRANS': 403} Chain breaks: 2 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'5H0': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.63, per 1000 atoms: 0.25 Number of scatterers: 14682 At special positions: 0 Unit cell: (97.324, 98.163, 119.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 83 16.00 P 4 15.00 O 2625 8.00 N 2389 7.00 C 9581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 669.0 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3366 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 67.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.556A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.552A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 196 through 221 removed outlier: 3.787A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.947A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.874A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 290 removed outlier: 3.603A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 362 Processing helix chain 'C' and resid 371 through 424 removed outlier: 5.370A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 475 removed outlier: 5.415A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 495 Processing helix chain 'C' and resid 545 through 550 removed outlier: 3.579A pdb=" N ILE C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 545 through 550' Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 601 Processing helix chain 'B' and resid 654 through 673 Processing helix chain 'B' and resid 674 through 679 Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.682A pdb=" N PHE B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 735 removed outlier: 4.019A pdb=" N ASN B 730 " --> pdb=" O LYS B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 744 removed outlier: 3.719A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Proline residue: B 764 - end of helix removed outlier: 4.048A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.542A pdb=" N LEU B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 814 removed outlier: 4.406A pdb=" N TYR B 789 " --> pdb=" O LYS B 785 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 814 " --> pdb=" O TYR B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 842 removed outlier: 3.797A pdb=" N CYS B 835 " --> pdb=" O SER B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 887 Processing helix chain 'B' and resid 887 through 907 Processing helix chain 'B' and resid 910 through 928 Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 941 through 960 removed outlier: 7.370A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 960 " --> pdb=" O ILE B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 977 Processing helix chain 'B' and resid 1029 through 1035 removed outlier: 3.770A pdb=" N ALA B1035 " --> pdb=" O SER B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1069 through 1084 Processing helix chain 'A' and resid 163 through 189 Proline residue: A 175 - end of helix removed outlier: 5.348A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.708A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.732A pdb=" N ASN A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 253 removed outlier: 4.043A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.970A pdb=" N LYS A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.857A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.689A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 removed outlier: 3.833A pdb=" N THR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 424 removed outlier: 4.316A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 458 through 475 removed outlier: 6.821A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 removed outlier: 3.533A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 588 through 607 Processing helix chain 'D' and resid 162 through 189 Proline residue: D 175 - end of helix removed outlier: 5.027A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.692A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 221 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.798A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.862A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG D 271 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 290 removed outlier: 3.834A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU D 289 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 458 through 475 removed outlier: 5.938A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 578 through 585 Processing helix chain 'D' and resid 588 through 606 Processing sheet with id=AA1, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'C' and resid 496 through 500 removed outlier: 7.040A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 520 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 536 through 538 removed outlier: 3.849A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 717 Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 7.956A pdb=" N ASN B1045 " --> pdb=" O GLY B1011 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLY B1011 " --> pdb=" O ASN B1045 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B1047 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B1009 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS B1049 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL B1007 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N PHE B1051 " --> pdb=" O GLY B1005 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY B1005 " --> pdb=" O PHE B1051 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1007 " --> pdb=" O THR B1021 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B1021 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1009 " --> pdb=" O LEU B1019 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B1017 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 983 removed outlier: 7.956A pdb=" N ASN B1045 " --> pdb=" O GLY B1011 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLY B1011 " --> pdb=" O ASN B1045 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B1047 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B1009 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS B1049 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL B1007 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N PHE B1051 " --> pdb=" O GLY B1005 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY B1005 " --> pdb=" O PHE B1051 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.865A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 520 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.303A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS A 507 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 524 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 537 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 526 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.795A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.592A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU D 524 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL D 537 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 526 " --> pdb=" O PHE D 535 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4527 1.34 - 1.47: 3805 1.47 - 1.59: 6557 1.59 - 1.71: 8 1.71 - 1.84: 140 Bond restraints: 15037 Sorted by residual: bond pdb=" O1A PCG C 701 " pdb=" PA PCG C 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.480 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O1A PCG B1301 " pdb=" PA PCG B1301 " ideal model delta sigma weight residual 1.582 1.481 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O1A PCG A1101 " pdb=" PA PCG A1101 " ideal model delta sigma weight residual 1.582 1.481 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1' PCG C 701 " pdb=" O4' PCG C 701 " ideal model delta sigma weight residual 1.409 1.482 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 15032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 19873 1.92 - 3.84: 381 3.84 - 5.76: 70 5.76 - 7.68: 40 7.68 - 9.60: 29 Bond angle restraints: 20393 Sorted by residual: angle pdb=" C GLY A 558 " pdb=" N ASN A 559 " pdb=" CA ASN A 559 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N GLU B 922 " pdb=" CA GLU B 922 " pdb=" CB GLU B 922 " ideal model delta sigma weight residual 110.16 116.13 -5.97 1.48e+00 4.57e-01 1.63e+01 angle pdb=" N CYS D 575 " pdb=" CA CYS D 575 " pdb=" C CYS D 575 " ideal model delta sigma weight residual 108.73 115.02 -6.29 1.63e+00 3.76e-01 1.49e+01 angle pdb=" C TYR A 196 " pdb=" N LEU A 197 " pdb=" CA LEU A 197 " ideal model delta sigma weight residual 120.82 126.45 -5.63 1.50e+00 4.44e-01 1.41e+01 angle pdb=" CB MET D 182 " pdb=" CG MET D 182 " pdb=" SD MET D 182 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 20388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 8588 28.54 - 57.07: 360 57.07 - 85.61: 28 85.61 - 114.15: 1 114.15 - 142.69: 16 Dihedral angle restraints: 8993 sinusoidal: 3745 harmonic: 5248 Sorted by residual: dihedral pdb=" C3' PCG C 701 " pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O1A PCG C 701 " ideal model delta sinusoidal sigma weight residual 151.41 -65.90 -142.69 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3' PCG A1101 " pdb=" O3' PCG A1101 " pdb=" PA PCG A1101 " pdb=" O1A PCG A1101 " ideal model delta sinusoidal sigma weight residual 151.41 -66.56 -142.03 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C3' PCG D 701 " pdb=" O3' PCG D 701 " pdb=" PA PCG D 701 " pdb=" O1A PCG D 701 " ideal model delta sinusoidal sigma weight residual 151.41 -66.97 -141.62 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 8990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 2255 0.136 - 0.271: 21 0.271 - 0.407: 1 0.407 - 0.543: 0 0.543 - 0.679: 4 Chirality restraints: 2281 Sorted by residual: chirality pdb=" PA PCG B1301 " pdb=" O2A PCG B1301 " pdb=" O3' PCG B1301 " pdb=" O5' PCG B1301 " both_signs ideal model delta sigma weight residual True 2.70 -3.38 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" PA PCG A1101 " pdb=" O2A PCG A1101 " pdb=" O3' PCG A1101 " pdb=" O5' PCG A1101 " both_signs ideal model delta sigma weight residual True 2.70 -3.37 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" PA PCG D 701 " pdb=" O2A PCG D 701 " pdb=" O3' PCG D 701 " pdb=" O5' PCG D 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.36 -0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 2278 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 267 " -0.056 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 268 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 860 " -0.024 2.00e-02 2.50e+03 2.03e-02 7.19e+00 pdb=" CG PHE B 860 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 860 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 860 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 860 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 860 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 860 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 684 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO B 685 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 685 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 685 " -0.033 5.00e-02 4.00e+02 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3530 2.79 - 3.32: 14086 3.32 - 3.84: 26032 3.84 - 4.37: 29691 4.37 - 4.90: 50920 Nonbonded interactions: 124259 Sorted by model distance: nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.260 3.040 nonbonded pdb=" OG SER C 501 " pdb=" OD2 ASP C 504 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 178 " pdb=" OD1 ASP C 204 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR C 334 " pdb=" O PHE C 342 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR B 892 " pdb=" OH TYR A 456 " model vdw 2.283 3.040 ... (remaining 124254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 605) selection = (chain 'C' and resid 156 through 605) selection = (chain 'D' and resid 156 through 605) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.600 Find NCS groups from input model: 0.280 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.004 0.104 15037 Z= 0.211 Angle : 0.767 9.600 20393 Z= 0.362 Chirality : 0.053 0.679 2281 Planarity : 0.005 0.086 2508 Dihedral : 16.047 142.686 5627 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1764 helix: 0.49 (0.14), residues: 1110 sheet: 0.19 (0.54), residues: 82 loop : 0.27 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 514 TYR 0.015 0.001 TYR B 797 PHE 0.046 0.002 PHE B 860 TRP 0.021 0.002 TRP A 168 HIS 0.010 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (15037) covalent geometry : angle 0.76717 / 0.36 (20393) hydrogen bonds : bond 0.12880 / 8.14 ( 919) hydrogen bonds : angle 5.51730 / 4.02 ( 2685) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.478 Fit side-chains REVERT: B 728 MET cc_start: 0.7139 (mtm) cc_final: 0.6874 (mtm) REVERT: A 269 GLU cc_start: 0.6106 (mp0) cc_final: 0.5761 (mt-10) REVERT: A 604 MET cc_start: 0.7340 (mtp) cc_final: 0.7108 (mtp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1063 time to fit residues: 38.8859 Evaluate side-chains 178 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 314 ASN A 243 ASN A 314 ASN A 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107791 restraints weight = 20182.159| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.45 r_work: 0.3120 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15037 Z= 0.155 Angle : 0.525 7.065 20393 Z= 0.272 Chirality : 0.040 0.176 2281 Planarity : 0.004 0.050 2508 Dihedral : 12.867 153.104 2104 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.69 % Allowed : 7.38 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1764 helix: 1.19 (0.15), residues: 1128 sheet: 0.13 (0.54), residues: 84 loop : 0.46 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.022 0.001 TYR B 787 PHE 0.017 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.006 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (15037) covalent geometry : angle 0.52507 / 0.27 (20393) hydrogen bonds : bond 0.03877 / 2.47 ( 919) hydrogen bonds : angle 4.19366 / 3.06 ( 2685) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: C 226 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7508 (mm-40) REVERT: C 483 CYS cc_start: 0.6735 (t) cc_final: 0.6140 (m) REVERT: A 269 GLU cc_start: 0.7335 (mp0) cc_final: 0.6436 (mt-10) REVERT: A 604 MET cc_start: 0.7557 (mtp) cc_final: 0.7206 (mtp) REVERT: D 234 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8213 (mp) REVERT: D 604 MET cc_start: 0.6732 (mpp) cc_final: 0.6455 (mpp) outliers start: 11 outliers final: 7 residues processed: 187 average time/residue: 0.1130 time to fit residues: 32.6666 Evaluate side-chains 176 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 0.0050 chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 444 ASN B 690 HIS A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106686 restraints weight = 20358.272| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.56 r_work: 0.3084 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15037 Z= 0.129 Angle : 0.482 5.585 20393 Z= 0.249 Chirality : 0.039 0.156 2281 Planarity : 0.003 0.051 2508 Dihedral : 12.703 152.211 2104 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.38 % Allowed : 9.50 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1764 helix: 1.48 (0.15), residues: 1128 sheet: 0.09 (0.54), residues: 84 loop : 0.47 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.018 0.001 TYR B 787 PHE 0.017 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15037) covalent geometry : angle 0.48197 / 0.25 (20393) hydrogen bonds : bond 0.03582 / 2.29 ( 919) hydrogen bonds : angle 3.96528 / 2.88 ( 2685) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.558 Fit side-chains REVERT: C 202 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7296 (mp) REVERT: C 483 CYS cc_start: 0.6806 (t) cc_final: 0.6240 (m) REVERT: A 269 GLU cc_start: 0.7628 (mp0) cc_final: 0.6578 (mt-10) REVERT: A 604 MET cc_start: 0.7570 (mtp) cc_final: 0.7264 (mtp) REVERT: D 234 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8192 (mp) REVERT: D 604 MET cc_start: 0.6625 (mpp) cc_final: 0.6134 (mpp) outliers start: 22 outliers final: 14 residues processed: 198 average time/residue: 0.1107 time to fit residues: 33.3044 Evaluate side-chains 187 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 33 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 166 optimal weight: 0.0270 chunk 124 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 GLN D 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102984 restraints weight = 20290.689| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.55 r_work: 0.3057 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15037 Z= 0.151 Angle : 0.495 6.269 20393 Z= 0.255 Chirality : 0.040 0.185 2281 Planarity : 0.003 0.052 2508 Dihedral : 12.655 151.545 2104 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.06 % Allowed : 10.69 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.20), residues: 1764 helix: 1.56 (0.15), residues: 1126 sheet: -0.19 (0.54), residues: 89 loop : 0.50 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 299 TYR 0.021 0.001 TYR D 349 PHE 0.020 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.006 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (15037) covalent geometry : angle 0.49525 / 0.26 (20393) hydrogen bonds : bond 0.03594 / 2.31 ( 919) hydrogen bonds : angle 3.95329 / 2.87 ( 2685) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7498 (mp) REVERT: C 483 CYS cc_start: 0.6798 (t) cc_final: 0.6162 (m) REVERT: C 594 MET cc_start: 0.7140 (tmm) cc_final: 0.6714 (tmm) REVERT: B 897 MET cc_start: 0.8178 (ttt) cc_final: 0.7921 (ttt) REVERT: B 1078 LYS cc_start: 0.7369 (tttt) cc_final: 0.6402 (mtpt) REVERT: A 269 GLU cc_start: 0.7978 (mp0) cc_final: 0.6698 (mt-10) REVERT: A 604 MET cc_start: 0.7539 (mtp) cc_final: 0.7249 (mtp) REVERT: D 234 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8232 (mp) REVERT: D 604 MET cc_start: 0.6508 (mpp) cc_final: 0.6159 (mpp) outliers start: 33 outliers final: 22 residues processed: 205 average time/residue: 0.1077 time to fit residues: 34.1422 Evaluate side-chains 194 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106429 restraints weight = 19835.801| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.36 r_work: 0.3045 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15037 Z= 0.197 Angle : 0.531 8.577 20393 Z= 0.275 Chirality : 0.041 0.168 2281 Planarity : 0.004 0.052 2508 Dihedral : 12.672 150.917 2104 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.25 % Allowed : 12.00 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1764 helix: 1.46 (0.15), residues: 1126 sheet: -0.31 (0.54), residues: 89 loop : 0.36 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 299 TYR 0.023 0.002 TYR D 349 PHE 0.024 0.002 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.007 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (15037) covalent geometry : angle 0.53077 / 0.27 (20393) hydrogen bonds : bond 0.03850 / 2.48 ( 919) hydrogen bonds : angle 4.07000 / 2.94 ( 2685) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7518 (mp) REVERT: C 483 CYS cc_start: 0.6829 (t) cc_final: 0.6237 (m) REVERT: C 594 MET cc_start: 0.7114 (tmm) cc_final: 0.6723 (tmm) REVERT: B 1078 LYS cc_start: 0.7269 (tttt) cc_final: 0.6189 (mtpt) REVERT: A 269 GLU cc_start: 0.8211 (mp0) cc_final: 0.6797 (mt-10) REVERT: A 604 MET cc_start: 0.7468 (mtp) cc_final: 0.7187 (mtp) REVERT: D 604 MET cc_start: 0.6570 (mpp) cc_final: 0.6200 (mpp) outliers start: 36 outliers final: 25 residues processed: 200 average time/residue: 0.1116 time to fit residues: 34.3554 Evaluate side-chains 193 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 132 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102030 restraints weight = 20049.159| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.45 r_work: 0.3095 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15037 Z= 0.182 Angle : 0.519 6.844 20393 Z= 0.268 Chirality : 0.041 0.183 2281 Planarity : 0.003 0.052 2508 Dihedral : 12.684 151.356 2104 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.06 % Allowed : 12.62 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1764 helix: 1.45 (0.15), residues: 1127 sheet: -0.29 (0.55), residues: 89 loop : 0.31 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 299 TYR 0.021 0.001 TYR D 349 PHE 0.023 0.001 PHE A 298 TRP 0.018 0.001 TRP A 168 HIS 0.006 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (15037) covalent geometry : angle 0.51947 / 0.27 (20393) hydrogen bonds : bond 0.03773 / 2.43 ( 919) hydrogen bonds : angle 4.05088 / 2.93 ( 2685) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7585 (mp) REVERT: C 483 CYS cc_start: 0.6891 (t) cc_final: 0.6377 (m) REVERT: C 594 MET cc_start: 0.7153 (tmm) cc_final: 0.6751 (tmm) REVERT: B 1078 LYS cc_start: 0.7301 (tttt) cc_final: 0.6233 (mtpt) REVERT: A 600 LYS cc_start: 0.7233 (tppt) cc_final: 0.6663 (tppt) REVERT: A 604 MET cc_start: 0.7494 (mtp) cc_final: 0.7198 (mtp) REVERT: D 604 MET cc_start: 0.6522 (mpp) cc_final: 0.6169 (mpp) outliers start: 33 outliers final: 24 residues processed: 197 average time/residue: 0.1163 time to fit residues: 34.8231 Evaluate side-chains 187 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104426 restraints weight = 19943.052| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.47 r_work: 0.3133 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15037 Z= 0.115 Angle : 0.473 6.577 20393 Z= 0.244 Chirality : 0.039 0.191 2281 Planarity : 0.003 0.052 2508 Dihedral : 12.598 152.574 2104 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.88 % Allowed : 13.31 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.20), residues: 1764 helix: 1.67 (0.15), residues: 1127 sheet: -0.21 (0.56), residues: 89 loop : 0.37 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 299 TYR 0.014 0.001 TYR D 349 PHE 0.019 0.001 PHE A 298 TRP 0.019 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (15037) covalent geometry : angle 0.47299 / 0.24 (20393) hydrogen bonds : bond 0.03495 / 2.24 ( 919) hydrogen bonds : angle 3.88072 / 2.81 ( 2685) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7569 (mp) REVERT: C 363 ILE cc_start: 0.7670 (mt) cc_final: 0.7368 (mt) REVERT: C 483 CYS cc_start: 0.6823 (t) cc_final: 0.6404 (m) REVERT: C 594 MET cc_start: 0.7164 (tmm) cc_final: 0.6777 (tmm) REVERT: B 1078 LYS cc_start: 0.7287 (tttt) cc_final: 0.6243 (mtpt) REVERT: A 269 GLU cc_start: 0.8033 (mp0) cc_final: 0.6699 (mt-10) REVERT: A 600 LYS cc_start: 0.7292 (tppt) cc_final: 0.6692 (tppt) REVERT: A 604 MET cc_start: 0.7463 (mtp) cc_final: 0.7193 (mtp) REVERT: D 574 PHE cc_start: 0.8431 (m-80) cc_final: 0.8215 (m-80) REVERT: D 604 MET cc_start: 0.6534 (mpp) cc_final: 0.5776 (mmp) outliers start: 30 outliers final: 19 residues processed: 202 average time/residue: 0.0985 time to fit residues: 30.7020 Evaluate side-chains 191 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 5.9990 chunk 104 optimal weight: 0.0050 chunk 157 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108302 restraints weight = 19930.831| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.37 r_work: 0.3089 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15037 Z= 0.115 Angle : 0.473 7.295 20393 Z= 0.243 Chirality : 0.039 0.168 2281 Planarity : 0.003 0.052 2508 Dihedral : 12.555 152.350 2104 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 1.69 % Allowed : 14.06 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.20), residues: 1764 helix: 1.77 (0.15), residues: 1127 sheet: -0.20 (0.59), residues: 79 loop : 0.39 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 299 TYR 0.019 0.001 TYR D 588 PHE 0.019 0.001 PHE A 298 TRP 0.018 0.001 TRP D 168 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15037) covalent geometry : angle 0.47276 / 0.24 (20393) hydrogen bonds : bond 0.03400 / 2.18 ( 919) hydrogen bonds : angle 3.82637 / 2.77 ( 2685) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7527 (mp) REVERT: C 483 CYS cc_start: 0.6888 (t) cc_final: 0.6280 (m) REVERT: C 594 MET cc_start: 0.7228 (tmm) cc_final: 0.6833 (tmm) REVERT: B 1078 LYS cc_start: 0.7302 (tttt) cc_final: 0.6252 (mtpt) REVERT: A 269 GLU cc_start: 0.8015 (mp0) cc_final: 0.6690 (mt-10) REVERT: A 600 LYS cc_start: 0.7228 (tppt) cc_final: 0.6648 (tppt) REVERT: A 604 MET cc_start: 0.7422 (mtp) cc_final: 0.7197 (mtp) REVERT: D 574 PHE cc_start: 0.8423 (m-80) cc_final: 0.8220 (m-80) REVERT: D 604 MET cc_start: 0.6541 (mpp) cc_final: 0.5802 (mmp) outliers start: 27 outliers final: 20 residues processed: 200 average time/residue: 0.0993 time to fit residues: 30.5991 Evaluate side-chains 191 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103525 restraints weight = 20110.962| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.44 r_work: 0.3127 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15037 Z= 0.151 Angle : 0.501 6.867 20393 Z= 0.259 Chirality : 0.040 0.238 2281 Planarity : 0.003 0.052 2508 Dihedral : 12.553 151.642 2104 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 1.56 % Allowed : 14.31 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.20), residues: 1764 helix: 1.72 (0.15), residues: 1127 sheet: -0.20 (0.59), residues: 79 loop : 0.36 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 299 TYR 0.023 0.001 TYR D 588 PHE 0.021 0.001 PHE A 298 TRP 0.017 0.001 TRP D 168 HIS 0.006 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (15037) covalent geometry : angle 0.50145 / 0.26 (20393) hydrogen bonds : bond 0.03548 / 2.29 ( 919) hydrogen bonds : angle 3.88851 / 2.81 ( 2685) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7595 (mp) REVERT: C 480 PHE cc_start: 0.8721 (m-80) cc_final: 0.8473 (m-80) REVERT: A 269 GLU cc_start: 0.8103 (mp0) cc_final: 0.6730 (mt-10) REVERT: A 600 LYS cc_start: 0.7261 (tppt) cc_final: 0.6710 (tppt) REVERT: A 604 MET cc_start: 0.7437 (mtp) cc_final: 0.7229 (mtp) REVERT: D 517 TYR cc_start: 0.8650 (m-80) cc_final: 0.8203 (m-80) REVERT: D 574 PHE cc_start: 0.8441 (m-80) cc_final: 0.8226 (m-80) REVERT: D 604 MET cc_start: 0.6464 (mpp) cc_final: 0.5680 (mmp) outliers start: 25 outliers final: 20 residues processed: 185 average time/residue: 0.0971 time to fit residues: 27.5514 Evaluate side-chains 188 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 102 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108589 restraints weight = 19819.124| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.40 r_work: 0.3091 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15037 Z= 0.110 Angle : 0.474 7.227 20393 Z= 0.244 Chirality : 0.039 0.223 2281 Planarity : 0.003 0.051 2508 Dihedral : 12.468 152.816 2104 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 1.62 % Allowed : 14.31 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1764 helix: 1.83 (0.15), residues: 1128 sheet: -0.10 (0.59), residues: 79 loop : 0.44 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 299 TYR 0.020 0.001 TYR D 588 PHE 0.018 0.001 PHE A 298 TRP 0.018 0.001 TRP A 168 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15037) covalent geometry : angle 0.47363 / 0.24 (20393) hydrogen bonds : bond 0.03341 / 2.15 ( 919) hydrogen bonds : angle 3.78177 / 2.74 ( 2685) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7536 (mp) REVERT: C 480 PHE cc_start: 0.8500 (m-80) cc_final: 0.8251 (m-80) REVERT: A 266 ASN cc_start: 0.7271 (p0) cc_final: 0.6815 (p0) REVERT: A 269 GLU cc_start: 0.8001 (mp0) cc_final: 0.6658 (mt-10) REVERT: A 600 LYS cc_start: 0.7171 (tppt) cc_final: 0.6594 (tppt) REVERT: A 604 MET cc_start: 0.7422 (mtp) cc_final: 0.7204 (mtp) REVERT: D 517 TYR cc_start: 0.8614 (m-80) cc_final: 0.8222 (m-80) REVERT: D 604 MET cc_start: 0.6521 (mpp) cc_final: 0.5761 (mmp) outliers start: 26 outliers final: 19 residues processed: 195 average time/residue: 0.1060 time to fit residues: 31.8120 Evaluate side-chains 188 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115083 restraints weight = 19470.932| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.28 r_work: 0.3114 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15037 Z= 0.109 Angle : 0.473 7.419 20393 Z= 0.243 Chirality : 0.039 0.222 2281 Planarity : 0.003 0.052 2508 Dihedral : 12.454 152.670 2104 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 1.38 % Allowed : 14.75 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1764 helix: 1.90 (0.15), residues: 1128 sheet: -0.01 (0.59), residues: 79 loop : 0.46 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.014 0.001 TYR D 349 PHE 0.019 0.001 PHE A 298 TRP 0.018 0.001 TRP D 168 HIS 0.006 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15037) covalent geometry : angle 0.47317 / 0.24 (20393) hydrogen bonds : bond 0.03301 / 2.12 ( 919) hydrogen bonds : angle 3.75461 / 2.72 ( 2685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.83 seconds wall clock time: 56 minutes 42.49 seconds (3402.49 seconds total)