Starting phenix.real_space_refine on Wed Mar 4 15:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhk_24464/03_2026/7rhk_24464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhk_24464/03_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_24464/03_2026/7rhk_24464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhk_24464/03_2026/7rhk_24464.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhk_24464/03_2026/7rhk_24464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhk_24464/03_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-5986/lib/python3.9/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: 3.62, 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: 1.34 Conformation dependent library (CDL) restraints added in 484.9 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: 0.39 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: 2.97 Time building geometry restraints manager: 1.67 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: 8609 28.54 - 57.07: 363 57.07 - 85.61: 28 85.61 - 114.15: 1 114.15 - 142.69: 16 Dihedral angle restraints: 9017 sinusoidal: 3769 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 9014 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: 2.770 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.460 Find NCS groups from input model: 0.270 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 16.041 142.686 5651 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 covalent geometry : bond 0.00447 (15037) covalent geometry : angle 0.76717 (20393) hydrogen bonds : bond 0.12880 ( 919) hydrogen bonds : angle 5.51730 ( 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 : 0.561 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: 0.0999 time to fit residues: 36.7022 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 : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 314 ASN B 690 HIS A 243 ASN A 314 ASN A 601 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105494 restraints weight = 20269.519| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.56 r_work: 0.3093 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1183 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= 0.154 Angle : 0.525 7.346 20393 Z= 0.271 Chirality : 0.040 0.171 2281 Planarity : 0.004 0.050 2508 Dihedral : 12.824 153.776 2128 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.62 % Allowed : 7.81 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1764 helix: 1.20 (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 0.003 0.000 ARG A 287 TYR 0.023 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 covalent geometry : bond 0.00349 (15037) covalent geometry : angle 0.52545 (20393) hydrogen bonds : bond 0.03786 ( 919) hydrogen bonds : angle 4.14777 ( 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 193 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 226 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7525 (mm-40) REVERT: C 483 CYS cc_start: 0.6811 (t) cc_final: 0.6296 (m) REVERT: A 269 GLU cc_start: 0.7395 (mp0) cc_final: 0.6468 (mt-10) REVERT: A 604 MET cc_start: 0.7587 (mtp) cc_final: 0.7261 (mtp) REVERT: D 234 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8238 (mp) REVERT: D 604 MET cc_start: 0.6716 (mpp) cc_final: 0.6420 (mpp) outliers start: 10 outliers final: 6 residues processed: 190 average time/residue: 0.1018 time to fit residues: 29.7657 Evaluate side-chains 176 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 955 ASN Chi-restraints excluded: chain D residue 221 THR 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: 9.9990 chunk 3 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 ASN A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102721 restraints weight = 20417.524| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.55 r_work: 0.3037 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15037 Z= 0.180 Angle : 0.525 6.087 20393 Z= 0.271 Chirality : 0.041 0.162 2281 Planarity : 0.004 0.051 2508 Dihedral : 12.674 151.182 2128 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.81 % Allowed : 9.62 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1764 helix: 1.36 (0.15), residues: 1123 sheet: -0.13 (0.53), residues: 89 loop : 0.48 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.021 0.001 TYR D 349 PHE 0.020 0.001 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.007 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00413 (15037) covalent geometry : angle 0.52509 (20393) hydrogen bonds : bond 0.03864 ( 919) hydrogen bonds : angle 4.09384 ( 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 215 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.451 Fit side-chains REVERT: C 202 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7338 (mp) REVERT: C 483 CYS cc_start: 0.6751 (t) cc_final: 0.6098 (m) REVERT: B 922 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: A 269 GLU cc_start: 0.7955 (mp0) cc_final: 0.6657 (mt-10) REVERT: A 604 MET cc_start: 0.7565 (mtp) cc_final: 0.7272 (mtp) REVERT: D 234 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8200 (mp) REVERT: D 604 MET cc_start: 0.6531 (mpp) cc_final: 0.6075 (mpp) outliers start: 29 outliers final: 19 residues processed: 205 average time/residue: 0.1084 time to fit residues: 33.8354 Evaluate side-chains 189 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 484 GLU 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 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 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: 8.9990 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105424 restraints weight = 20212.738| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.55 r_work: 0.3095 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15037 Z= 0.105 Angle : 0.463 8.102 20393 Z= 0.238 Chirality : 0.039 0.213 2281 Planarity : 0.003 0.051 2508 Dihedral : 12.597 152.965 2128 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.62 % Allowed : 11.62 % Favored : 86.75 % 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: 1.72 (0.20), residues: 1764 helix: 1.62 (0.15), residues: 1128 sheet: 0.00 (0.55), residues: 84 loop : 0.50 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 220 TYR 0.016 0.001 TYR B 682 PHE 0.017 0.001 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00230 (15037) covalent geometry : angle 0.46303 (20393) hydrogen bonds : bond 0.03388 ( 919) hydrogen bonds : angle 3.85182 ( 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: 26 poor density : 192 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7478 (mp) REVERT: C 483 CYS cc_start: 0.6777 (t) cc_final: 0.6229 (m) REVERT: C 594 MET cc_start: 0.7140 (tmm) cc_final: 0.6789 (tmm) REVERT: B 922 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: A 269 GLU cc_start: 0.7709 (mp0) cc_final: 0.6581 (mt-10) REVERT: A 604 MET cc_start: 0.7564 (mtp) cc_final: 0.7240 (mtp) REVERT: D 234 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8233 (mp) REVERT: D 604 MET cc_start: 0.6477 (mpp) cc_final: 0.6118 (mpp) outliers start: 26 outliers final: 13 residues processed: 206 average time/residue: 0.1108 time to fit residues: 34.7617 Evaluate side-chains 191 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 399 MET Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain D residue 158 ILE 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: 4.9990 chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 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 = 0.3507 r_free = 0.3507 target = 0.129178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104038 restraints weight = 20045.786| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.50 r_work: 0.3037 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15037 Z= 0.169 Angle : 0.509 6.222 20393 Z= 0.264 Chirality : 0.040 0.160 2281 Planarity : 0.003 0.051 2508 Dihedral : 12.588 150.885 2128 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.12 % Allowed : 12.00 % Favored : 85.88 % 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: 1.61 (0.20), residues: 1764 helix: 1.56 (0.15), residues: 1128 sheet: -0.19 (0.54), residues: 89 loop : 0.43 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.022 0.001 TYR D 349 PHE 0.023 0.001 PHE A 298 TRP 0.016 0.001 TRP D 168 HIS 0.007 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00387 (15037) covalent geometry : angle 0.50942 (20393) hydrogen bonds : bond 0.03679 ( 919) hydrogen bonds : angle 3.97952 ( 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 213 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.556 Fit side-chains REVERT: C 202 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7502 (mp) REVERT: C 483 CYS cc_start: 0.6826 (t) cc_final: 0.6385 (m) REVERT: B 897 MET cc_start: 0.8275 (ttt) cc_final: 0.8048 (ttt) REVERT: B 922 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: B 1078 LYS cc_start: 0.7324 (tttt) cc_final: 0.6238 (mtpt) REVERT: A 269 GLU cc_start: 0.8135 (mp0) cc_final: 0.6798 (mt-10) REVERT: A 421 MET cc_start: 0.8870 (mtm) cc_final: 0.8654 (mtm) REVERT: A 604 MET cc_start: 0.7441 (mtp) cc_final: 0.7169 (mtp) REVERT: D 234 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8210 (mp) REVERT: D 299 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7655 (ttp-170) REVERT: D 604 MET cc_start: 0.6575 (mpp) cc_final: 0.6179 (mpp) outliers start: 34 outliers final: 23 residues processed: 201 average time/residue: 0.1015 time to fit residues: 31.1358 Evaluate side-chains 198 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 447 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 604 MET 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 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 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 158 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 132 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107823 restraints weight = 19927.067| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.43 r_work: 0.3081 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15037 Z= 0.115 Angle : 0.464 6.403 20393 Z= 0.240 Chirality : 0.039 0.149 2281 Planarity : 0.003 0.051 2508 Dihedral : 12.547 152.436 2128 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.94 % Allowed : 12.56 % Favored : 85.50 % 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: 1.76 (0.20), residues: 1764 helix: 1.68 (0.15), residues: 1127 sheet: -0.05 (0.58), residues: 79 loop : 0.45 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.015 0.001 TYR D 349 PHE 0.019 0.001 PHE A 298 TRP 0.018 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00257 (15037) covalent geometry : angle 0.46407 (20393) hydrogen bonds : bond 0.03419 ( 919) hydrogen bonds : angle 3.85688 ( 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 217 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.565 Fit side-chains REVERT: C 202 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7526 (mp) REVERT: C 483 CYS cc_start: 0.6829 (t) cc_final: 0.6368 (m) REVERT: C 594 MET cc_start: 0.7225 (tmm) cc_final: 0.6825 (tmm) REVERT: B 897 MET cc_start: 0.8279 (ttt) cc_final: 0.8057 (ttt) REVERT: B 922 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: B 1078 LYS cc_start: 0.7281 (tttt) cc_final: 0.6262 (mtpt) REVERT: A 269 GLU cc_start: 0.8003 (mp0) cc_final: 0.6682 (mt-10) REVERT: A 421 MET cc_start: 0.8850 (mtm) cc_final: 0.8620 (mtm) REVERT: A 604 MET cc_start: 0.7507 (mtp) cc_final: 0.7233 (mtp) REVERT: D 574 PHE cc_start: 0.8435 (m-80) cc_final: 0.8194 (m-80) REVERT: D 604 MET cc_start: 0.6560 (mpp) cc_final: 0.6167 (mpp) outliers start: 31 outliers final: 16 residues processed: 207 average time/residue: 0.1082 time to fit residues: 34.4559 Evaluate side-chains 191 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 386 VAL Chi-restraints excluded: chain C residue 399 MET 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 760 LEU 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 366 THR Chi-restraints excluded: chain D residue 158 ILE 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: 4.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 72 optimal weight: 0.0270 chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3568 r_free = 0.3568 target = 0.134040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110843 restraints weight = 19753.792| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.35 r_work: 0.3109 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1910 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= 0.101 Angle : 0.456 7.677 20393 Z= 0.235 Chirality : 0.038 0.151 2281 Planarity : 0.003 0.051 2508 Dihedral : 12.497 152.551 2128 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.00 % Allowed : 12.81 % Favored : 85.19 % 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: 1.92 (0.20), residues: 1764 helix: 1.81 (0.15), residues: 1128 sheet: -0.08 (0.58), residues: 79 loop : 0.51 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 299 TYR 0.014 0.001 TYR B 787 PHE 0.018 0.001 PHE A 298 TRP 0.017 0.001 TRP D 168 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00219 (15037) covalent geometry : angle 0.45566 (20393) hydrogen bonds : bond 0.03286 ( 919) hydrogen bonds : angle 3.77376 ( 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 218 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.579 Fit side-chains REVERT: C 202 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7569 (mp) REVERT: C 483 CYS cc_start: 0.6875 (t) cc_final: 0.6572 (m) REVERT: C 487 LEU cc_start: 0.7118 (tp) cc_final: 0.6706 (pp) REVERT: C 594 MET cc_start: 0.7287 (tmm) cc_final: 0.6933 (tmm) REVERT: B 897 MET cc_start: 0.8236 (ttt) cc_final: 0.8026 (ttt) REVERT: B 922 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: B 1078 LYS cc_start: 0.7305 (tttt) cc_final: 0.6277 (mtpt) REVERT: A 269 GLU cc_start: 0.7935 (mp0) cc_final: 0.6647 (mt-10) REVERT: A 600 LYS cc_start: 0.7167 (tppt) cc_final: 0.6575 (tppt) REVERT: A 604 MET cc_start: 0.7482 (mtp) cc_final: 0.7267 (mtp) REVERT: D 299 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7510 (ttp-170) REVERT: D 604 MET cc_start: 0.6574 (mpp) cc_final: 0.5825 (mmp) outliers start: 32 outliers final: 17 residues processed: 205 average time/residue: 0.1084 time to fit residues: 34.0641 Evaluate side-chains 194 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 399 MET Chi-restraints excluded: chain C residue 484 GLU 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 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 234 LEU 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: 0.7980 chunk 104 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3549 r_free = 0.3549 target = 0.132699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109165 restraints weight = 19892.865| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.38 r_work: 0.3082 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15037 Z= 0.128 Angle : 0.479 7.217 20393 Z= 0.247 Chirality : 0.039 0.195 2281 Planarity : 0.003 0.051 2508 Dihedral : 12.483 151.876 2128 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 13.31 % Favored : 84.94 % 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: 1.89 (0.20), residues: 1764 helix: 1.80 (0.15), residues: 1131 sheet: -0.08 (0.59), residues: 79 loop : 0.47 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 478 TYR 0.023 0.001 TYR D 588 PHE 0.020 0.001 PHE A 298 TRP 0.016 0.001 TRP D 168 HIS 0.007 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00292 (15037) covalent geometry : angle 0.47880 (20393) hydrogen bonds : bond 0.03385 ( 919) hydrogen bonds : angle 3.80576 ( 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 205 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7549 (mp) REVERT: C 483 CYS cc_start: 0.6929 (t) cc_final: 0.6569 (m) REVERT: C 487 LEU cc_start: 0.7087 (tp) cc_final: 0.6668 (pp) REVERT: C 594 MET cc_start: 0.7235 (tmm) cc_final: 0.6904 (tmm) REVERT: B 922 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: B 1078 LYS cc_start: 0.7284 (tttt) cc_final: 0.6194 (mtpt) REVERT: A 269 GLU cc_start: 0.7994 (mp0) cc_final: 0.6671 (mt-10) REVERT: A 600 LYS cc_start: 0.7158 (tppt) cc_final: 0.6575 (tppt) REVERT: A 604 MET cc_start: 0.7490 (mtp) cc_final: 0.7287 (mtp) REVERT: D 299 ARG cc_start: 0.7900 (ttp-170) cc_final: 0.7444 (ttp-170) REVERT: D 604 MET cc_start: 0.6519 (mpp) cc_final: 0.5778 (mmp) outliers start: 28 outliers final: 19 residues processed: 193 average time/residue: 0.1066 time to fit residues: 31.7098 Evaluate side-chains 193 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 386 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU 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 B residue 1058 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP 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 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: 4.9990 chunk 17 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3550 r_free = 0.3550 target = 0.132608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108969 restraints weight = 20005.374| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.36 r_work: 0.3095 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15037 Z= 0.120 Angle : 0.476 9.773 20393 Z= 0.244 Chirality : 0.039 0.263 2281 Planarity : 0.003 0.050 2508 Dihedral : 12.458 152.240 2128 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 1.56 % Allowed : 13.56 % Favored : 84.88 % 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: 1.93 (0.20), residues: 1764 helix: 1.83 (0.15), residues: 1131 sheet: -0.09 (0.59), residues: 79 loop : 0.48 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 478 TYR 0.022 0.001 TYR D 588 PHE 0.019 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 covalent geometry : bond 0.00271 (15037) covalent geometry : angle 0.47570 (20393) hydrogen bonds : bond 0.03343 ( 919) hydrogen bonds : angle 3.78276 ( 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 199 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.439 Fit side-chains REVERT: C 202 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7564 (mp) REVERT: C 483 CYS cc_start: 0.6995 (t) cc_final: 0.6574 (m) REVERT: C 487 LEU cc_start: 0.7054 (tp) cc_final: 0.6654 (pp) REVERT: C 594 MET cc_start: 0.7210 (tmm) cc_final: 0.6874 (tmm) REVERT: B 922 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: A 269 GLU cc_start: 0.7976 (mp0) cc_final: 0.6658 (mt-10) REVERT: A 421 MET cc_start: 0.8832 (mtm) cc_final: 0.8628 (mtm) REVERT: A 600 LYS cc_start: 0.7165 (tppt) cc_final: 0.6625 (tppt) REVERT: D 604 MET cc_start: 0.6523 (mpp) cc_final: 0.5754 (mmp) outliers start: 25 outliers final: 19 residues processed: 188 average time/residue: 0.1057 time to fit residues: 30.6783 Evaluate side-chains 189 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 386 VAL Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU 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 760 LEU 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 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 174 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 102 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 174 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3588 r_free = 0.3588 target = 0.136077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112060 restraints weight = 19535.390| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.35 r_work: 0.3104 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15037 Z= 0.120 Angle : 0.480 8.077 20393 Z= 0.247 Chirality : 0.039 0.240 2281 Planarity : 0.003 0.050 2508 Dihedral : 12.424 152.419 2128 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 1.50 % Allowed : 13.69 % 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: 1.95 (0.20), residues: 1764 helix: 1.85 (0.15), residues: 1130 sheet: -0.08 (0.59), residues: 79 loop : 0.49 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 478 TYR 0.018 0.001 TYR D 588 PHE 0.019 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 covalent geometry : bond 0.00272 (15037) covalent geometry : angle 0.48013 (20393) hydrogen bonds : bond 0.03344 ( 919) hydrogen bonds : angle 3.77529 ( 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 199 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.549 Fit side-chains REVERT: C 202 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7550 (mp) REVERT: C 483 CYS cc_start: 0.7016 (t) cc_final: 0.6498 (m) REVERT: C 487 LEU cc_start: 0.7053 (tp) cc_final: 0.6661 (pp) REVERT: C 594 MET cc_start: 0.7229 (tmm) cc_final: 0.6907 (tmm) REVERT: B 922 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: B 1078 LYS cc_start: 0.7373 (tttt) cc_final: 0.6292 (mtpt) REVERT: A 269 GLU cc_start: 0.7964 (mp0) cc_final: 0.6657 (mt-10) REVERT: D 604 MET cc_start: 0.6536 (mpp) cc_final: 0.5764 (mmp) outliers start: 24 outliers final: 21 residues processed: 192 average time/residue: 0.1067 time to fit residues: 31.7806 Evaluate side-chains 195 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE 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 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU 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 760 LEU 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 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 174 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: 0.0970 chunk 45 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 chunk 148 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 670 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115496 restraints weight = 19625.290| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.30 r_work: 0.3133 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2018 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= 0.096 Angle : 0.461 7.443 20393 Z= 0.236 Chirality : 0.039 0.219 2281 Planarity : 0.003 0.050 2508 Dihedral : 12.375 153.144 2128 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 1.25 % Allowed : 14.25 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1764 helix: 1.95 (0.15), residues: 1130 sheet: -0.02 (0.58), residues: 79 loop : 0.52 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1082 TYR 0.013 0.001 TYR B 787 PHE 0.017 0.001 PHE A 298 TRP 0.018 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00210 (15037) covalent geometry : angle 0.46087 (20393) hydrogen bonds : bond 0.03147 ( 919) hydrogen bonds : angle 3.69359 ( 2685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.86 seconds wall clock time: 55 minutes 50.25 seconds (3350.25 seconds total)