Starting phenix.real_space_refine on Fri Jul 3 01:28:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzc_18774/07_2026/8qzc_18774.cif" } resolution = 3.29 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= 0.002 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 Ca 4 9.91 5 S 72 5.16 5 C 7472 2.51 5 N 1888 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 11468 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5732 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Chain: "B" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5732 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.75, per 1000 atoms: 0.24 Number of scatterers: 11468 At special positions: 0 Unit cell: (90.283, 121.915, 113.348, 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) Ca 4 19.99 S 72 16.00 O 2032 8.00 N 1888 7.00 C 7472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.02 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.02 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 534.9 milliseconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 67.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 166 through 180 removed outlier: 4.041A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.643A pdb=" N LYS A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.648A pdb=" N SER A 225 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.672A pdb=" N PHE A 240 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 241 " --> pdb=" O ASP A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 241' Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.650A pdb=" N VAL A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 316 through 358 removed outlier: 7.524A pdb=" N GLU A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N LYS A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.665A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 439 removed outlier: 3.531A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 Processing helix chain 'A' and resid 489 through 527 removed outlier: 3.724A pdb=" N ALA A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 569 removed outlier: 4.070A pdb=" N GLU A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 630 through 651 removed outlier: 3.937A pdb=" N LYS A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 693 removed outlier: 3.728A pdb=" N VAL A 689 " --> pdb=" O GLN A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 removed outlier: 3.652A pdb=" N GLU A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.938A pdb=" N VAL A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.933A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.783A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 removed outlier: 3.906A pdb=" N ARG A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.011A pdb=" N MET B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.847A pdb=" N HIS B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.543A pdb=" N SER B 225 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.726A pdb=" N PHE B 240 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 241 " --> pdb=" O ASP B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 241' Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.631A pdb=" N VAL B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 311 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 316 through 358 removed outlier: 7.512A pdb=" N GLU B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N LYS B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.662A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 439 removed outlier: 3.523A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 465 Processing helix chain 'B' and resid 489 through 527 removed outlier: 3.715A pdb=" N ALA B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 569 removed outlier: 4.068A pdb=" N GLU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 569 " --> pdb=" O THR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 630 through 651 removed outlier: 3.959A pdb=" N LYS B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 693 removed outlier: 3.701A pdb=" N VAL B 689 " --> pdb=" O GLN B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 716 removed outlier: 3.655A pdb=" N GLU B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 744 removed outlier: 3.921A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.942A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.780A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 removed outlier: 3.893A pdb=" N ARG B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 3.893A pdb=" N ALA A 279 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190 removed outlier: 3.525A pdb=" N THR A 187 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.939A pdb=" N ALA B 279 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 removed outlier: 3.583A pdb=" N THR B 187 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813 661 hydrogen bonds defined for protein. 1947 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: 1.81 Time building geometry restraints manager: 1.17 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: 3562 1.34 - 1.46: 2914 1.46 - 1.58: 5160 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11754 Sorted by residual: bond pdb=" CB GLU A 555 " pdb=" CG GLU A 555 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CB GLU B 555 " pdb=" CG GLU B 555 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" SD MET A 416 " pdb=" CE MET A 416 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.02e+00 bond pdb=" SD MET B 416 " pdb=" CE MET B 416 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 2.01e+00 bond pdb=" CB ASP B 883 " pdb=" CG ASP B 883 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 ... (remaining 11749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 15678 2.68 - 5.37: 178 5.37 - 8.05: 44 8.05 - 10.74: 6 10.74 - 13.42: 6 Bond angle restraints: 15912 Sorted by residual: angle pdb=" CB MET A 424 " pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C TYR B 288 " pdb=" N GLU B 289 " pdb=" CA GLU B 289 " ideal model delta sigma weight residual 122.08 127.90 -5.82 1.47e+00 4.63e-01 1.56e+01 angle pdb=" CB MET B 424 " pdb=" CG MET B 424 " pdb=" SD MET B 424 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C TYR A 288 " pdb=" N GLU A 289 " pdb=" CA GLU A 289 " ideal model delta sigma weight residual 122.08 127.81 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" CA LEU B 191 " pdb=" CB LEU B 191 " pdb=" CG LEU B 191 " ideal model delta sigma weight residual 116.30 129.72 -13.42 3.50e+00 8.16e-02 1.47e+01 ... (remaining 15907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 6166 16.03 - 32.06: 702 32.06 - 48.08: 127 48.08 - 64.11: 21 64.11 - 80.14: 6 Dihedral angle restraints: 7022 sinusoidal: 2870 harmonic: 4152 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -149.60 63.60 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -149.37 63.37 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -46.12 -39.88 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1314 0.051 - 0.102: 352 0.102 - 0.154: 80 0.154 - 0.205: 3 0.205 - 0.256: 5 Chirality restraints: 1754 Sorted by residual: chirality pdb=" CA GLU B 425 " pdb=" N GLU B 425 " pdb=" C GLU B 425 " pdb=" CB GLU B 425 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL A 569 " pdb=" CA VAL A 569 " pdb=" CG1 VAL A 569 " pdb=" CG2 VAL A 569 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL B 750 " pdb=" CA VAL B 750 " pdb=" CG1 VAL B 750 " pdb=" CG2 VAL B 750 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1751 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 176 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 177 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 176 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO B 177 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 406 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO B 407 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.025 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2328 2.78 - 3.31: 10850 3.31 - 3.84: 18851 3.84 - 4.37: 21116 4.37 - 4.90: 37307 Nonbonded interactions: 90452 Sorted by model distance: nonbonded pdb=" O VAL B 590 " pdb=" OG1 THR B 594 " model vdw 2.246 3.040 nonbonded pdb=" O VAL A 590 " pdb=" OG1 THR A 594 " model vdw 2.249 3.040 nonbonded pdb=" O LYS A 175 " pdb=" OG1 THR A 178 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 387 " pdb=" OD2 ASP A 828 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 387 " pdb=" OD2 ASP B 828 " model vdw 2.291 3.040 ... (remaining 90447 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.047 11762 Z= 0.187 Angle : 0.816 13.424 15928 Z= 0.421 Chirality : 0.049 0.256 1754 Planarity : 0.006 0.058 1998 Dihedral : 13.360 80.141 4310 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.37 (0.20), residues: 1382 helix: -0.05 (0.16), residues: 856 sheet: -1.79 (0.99), residues: 28 loop : -2.35 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 128 TYR 0.026 0.002 TYR B 222 PHE 0.028 0.002 PHE B 324 TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (11754) covalent geometry : angle 0.81325 / 0.42 (15912) SS BOND : bond 0.00489 / 0.22 ( 8) SS BOND : angle 2.21171 / 1.18 ( 16) hydrogen bonds : bond 0.09950 / 6.62 ( 661) hydrogen bonds : angle 5.81106 / 3.93 ( 1947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.323 Fit side-chains REVERT: A 827 LEU cc_start: 0.7498 (mt) cc_final: 0.7217 (mp) REVERT: A 909 MET cc_start: 0.5081 (ttm) cc_final: 0.3630 (tpt) REVERT: B 827 LEU cc_start: 0.7553 (mt) cc_final: 0.7310 (mp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1039 time to fit residues: 25.7091 Evaluate side-chains 130 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.187721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144754 restraints weight = 13995.091| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.90 r_work: 0.3579 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11762 Z= 0.187 Angle : 0.622 8.499 15928 Z= 0.324 Chirality : 0.043 0.183 1754 Planarity : 0.004 0.048 1998 Dihedral : 4.303 16.228 1546 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.88 % Allowed : 7.85 % Favored : 91.27 % 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: -0.39 (0.22), residues: 1382 helix: 0.87 (0.17), residues: 854 sheet: -2.85 (0.59), residues: 58 loop : -2.03 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.015 0.002 TYR B 838 PHE 0.019 0.002 PHE A 126 TRP 0.015 0.002 TRP A 427 HIS 0.008 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (11754) covalent geometry : angle 0.61927 / 0.32 (15912) SS BOND : bond 0.00296 / 0.15 ( 8) SS BOND : angle 1.99072 / 1.10 ( 16) hydrogen bonds : bond 0.04284 / 2.77 ( 661) hydrogen bonds : angle 4.24834 / 2.93 ( 1947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.459 Fit side-chains REVERT: A 215 GLN cc_start: 0.7402 (pp30) cc_final: 0.6424 (pp30) REVERT: A 691 PHE cc_start: 0.8420 (t80) cc_final: 0.8214 (t80) REVERT: A 752 ILE cc_start: 0.8254 (tt) cc_final: 0.7608 (mm) REVERT: B 215 GLN cc_start: 0.7497 (pp30) cc_final: 0.7246 (pt0) REVERT: B 752 ILE cc_start: 0.8215 (tt) cc_final: 0.7579 (mm) outliers start: 11 outliers final: 9 residues processed: 150 average time/residue: 0.1072 time to fit residues: 23.8478 Evaluate side-chains 142 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 733 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.196380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.157926 restraints weight = 14252.271| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.91 r_work: 0.3716 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11762 Z= 0.122 Angle : 0.553 7.751 15928 Z= 0.284 Chirality : 0.040 0.194 1754 Planarity : 0.004 0.046 1998 Dihedral : 4.040 14.272 1546 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.80 % Allowed : 10.26 % Favored : 88.94 % 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: 0.10 (0.22), residues: 1382 helix: 1.35 (0.17), residues: 854 sheet: -3.14 (0.59), residues: 48 loop : -1.99 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.011 0.001 TYR B 355 PHE 0.028 0.001 PHE A 126 TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11754) covalent geometry : angle 0.55096 / 0.28 (15912) SS BOND : bond 0.00283 / 0.13 ( 8) SS BOND : angle 1.45534 / 0.78 ( 16) hydrogen bonds : bond 0.03731 / 2.40 ( 661) hydrogen bonds : angle 3.96308 / 2.73 ( 1947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.464 Fit side-chains REVERT: A 215 GLN cc_start: 0.7285 (pp30) cc_final: 0.6364 (pp30) REVERT: A 691 PHE cc_start: 0.8444 (t80) cc_final: 0.8208 (t80) REVERT: A 752 ILE cc_start: 0.8339 (tt) cc_final: 0.7810 (mm) REVERT: A 909 MET cc_start: 0.4880 (ttm) cc_final: 0.3545 (tpt) REVERT: B 215 GLN cc_start: 0.7427 (pp30) cc_final: 0.7187 (pt0) REVERT: B 752 ILE cc_start: 0.8215 (tt) cc_final: 0.7618 (mm) outliers start: 10 outliers final: 4 residues processed: 148 average time/residue: 0.1033 time to fit residues: 22.7159 Evaluate side-chains 135 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.196611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.156370 restraints weight = 14406.167| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.73 r_work: 0.3749 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11762 Z= 0.122 Angle : 0.561 7.940 15928 Z= 0.288 Chirality : 0.040 0.195 1754 Planarity : 0.003 0.045 1998 Dihedral : 4.051 22.063 1546 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.72 % Allowed : 11.86 % Favored : 87.42 % 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: 0.32 (0.22), residues: 1382 helix: 1.53 (0.17), residues: 854 sheet: -3.10 (0.60), residues: 48 loop : -1.93 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.011 0.001 TYR A 838 PHE 0.027 0.001 PHE A 126 TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11754) covalent geometry : angle 0.55690 / 0.29 (15912) SS BOND : bond 0.00433 / 0.19 ( 8) SS BOND : angle 2.12170 / 1.14 ( 16) hydrogen bonds : bond 0.03669 / 2.35 ( 661) hydrogen bonds : angle 3.90305 / 2.69 ( 1947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.7207 (pp30) cc_final: 0.6897 (pt0) REVERT: A 752 ILE cc_start: 0.8376 (tt) cc_final: 0.7838 (mm) REVERT: A 909 MET cc_start: 0.4907 (ttm) cc_final: 0.3573 (tpt) REVERT: B 752 ILE cc_start: 0.8216 (tt) cc_final: 0.7585 (mm) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.1058 time to fit residues: 23.3335 Evaluate side-chains 140 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 73 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.192567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.154224 restraints weight = 14254.262| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.00 r_work: 0.3671 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11762 Z= 0.169 Angle : 0.605 8.452 15928 Z= 0.312 Chirality : 0.042 0.175 1754 Planarity : 0.004 0.043 1998 Dihedral : 4.177 20.441 1546 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.60 % Allowed : 11.70 % Favored : 86.70 % 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: 0.22 (0.22), residues: 1382 helix: 1.43 (0.17), residues: 854 sheet: -2.95 (0.61), residues: 58 loop : -1.90 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 686 TYR 0.014 0.002 TYR B 838 PHE 0.033 0.002 PHE A 126 TRP 0.014 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (11754) covalent geometry : angle 0.60082 / 0.31 (15912) SS BOND : bond 0.00227 / 0.11 ( 8) SS BOND : angle 2.28237 / 1.22 ( 16) hydrogen bonds : bond 0.04064 / 2.61 ( 661) hydrogen bonds : angle 4.00509 / 2.76 ( 1947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.498 Fit side-chains REVERT: A 215 GLN cc_start: 0.7246 (pp30) cc_final: 0.6990 (pt0) REVERT: A 730 ASN cc_start: 0.8377 (t0) cc_final: 0.8095 (m-40) REVERT: A 752 ILE cc_start: 0.8403 (tt) cc_final: 0.7828 (mm) REVERT: B 730 ASN cc_start: 0.8379 (t0) cc_final: 0.8091 (m-40) REVERT: B 752 ILE cc_start: 0.8256 (tt) cc_final: 0.7637 (mm) outliers start: 20 outliers final: 15 residues processed: 155 average time/residue: 0.1041 time to fit residues: 23.9071 Evaluate side-chains 148 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 134 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 103 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 0.0000 chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.197670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155271 restraints weight = 14298.383| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.91 r_work: 0.3768 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11762 Z= 0.106 Angle : 0.545 8.320 15928 Z= 0.277 Chirality : 0.040 0.226 1754 Planarity : 0.003 0.043 1998 Dihedral : 3.925 17.375 1546 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.04 % Allowed : 12.42 % Favored : 86.54 % 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: 0.61 (0.23), residues: 1382 helix: 1.78 (0.18), residues: 854 sheet: -2.91 (0.61), residues: 58 loop : -1.81 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.011 0.001 TYR A 687 PHE 0.030 0.001 PHE A 126 TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (11754) covalent geometry : angle 0.54270 / 0.28 (15912) SS BOND : bond 0.00275 / 0.13 ( 8) SS BOND : angle 1.77270 / 0.96 ( 16) hydrogen bonds : bond 0.03470 / 2.20 ( 661) hydrogen bonds : angle 3.81003 / 2.62 ( 1947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.458 Fit side-chains REVERT: A 215 GLN cc_start: 0.7140 (pp30) cc_final: 0.6933 (pt0) REVERT: A 752 ILE cc_start: 0.8390 (tt) cc_final: 0.8172 (tp) REVERT: A 909 MET cc_start: 0.4775 (ttm) cc_final: 0.3499 (tpt) REVERT: B 730 ASN cc_start: 0.8219 (t0) cc_final: 0.8016 (m-40) outliers start: 13 outliers final: 6 residues processed: 149 average time/residue: 0.1111 time to fit residues: 24.0796 Evaluate side-chains 138 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 130 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.197486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155010 restraints weight = 14210.176| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.86 r_work: 0.3764 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11762 Z= 0.111 Angle : 0.547 8.604 15928 Z= 0.278 Chirality : 0.040 0.201 1754 Planarity : 0.003 0.044 1998 Dihedral : 3.890 16.257 1546 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.04 % Allowed : 13.94 % Favored : 85.02 % 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: 0.70 (0.23), residues: 1382 helix: 1.85 (0.18), residues: 854 sheet: -2.86 (0.62), residues: 58 loop : -1.77 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.012 0.001 TYR A 687 PHE 0.031 0.001 PHE A 126 TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11754) covalent geometry : angle 0.54463 / 0.28 (15912) SS BOND : bond 0.00256 / 0.12 ( 8) SS BOND : angle 1.70702 / 0.92 ( 16) hydrogen bonds : bond 0.03519 / 2.25 ( 661) hydrogen bonds : angle 3.78458 / 2.61 ( 1947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.448 Fit side-chains REVERT: A 909 MET cc_start: 0.4793 (ttm) cc_final: 0.3549 (tpt) REVERT: B 730 ASN cc_start: 0.8209 (t0) cc_final: 0.7988 (m-40) outliers start: 13 outliers final: 10 residues processed: 148 average time/residue: 0.1183 time to fit residues: 25.0196 Evaluate side-chains 141 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 206 GLN B 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.195330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155606 restraints weight = 14229.208| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.86 r_work: 0.3710 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 0.038 11762 Z= 0.135 Angle : 0.570 8.849 15928 Z= 0.292 Chirality : 0.040 0.181 1754 Planarity : 0.003 0.044 1998 Dihedral : 3.953 16.454 1546 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.12 % Allowed : 14.34 % Favored : 84.54 % 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: 0.64 (0.23), residues: 1382 helix: 1.79 (0.18), residues: 854 sheet: -2.94 (0.63), residues: 58 loop : -1.77 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.011 0.001 TYR A 687 PHE 0.027 0.001 PHE A 126 TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11754) covalent geometry : angle 0.56787 / 0.29 (15912) SS BOND : bond 0.00209 / 0.10 ( 8) SS BOND : angle 1.75526 / 0.94 ( 16) hydrogen bonds : bond 0.03727 / 2.38 ( 661) hydrogen bonds : angle 3.85109 / 2.66 ( 1947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.458 Fit side-chains REVERT: A 175 LYS cc_start: 0.7940 (tptm) cc_final: 0.7346 (ttpp) REVERT: A 176 MET cc_start: 0.5911 (ttt) cc_final: 0.5679 (ttt) REVERT: A 909 MET cc_start: 0.4881 (ttm) cc_final: 0.3681 (tpt) REVERT: B 730 ASN cc_start: 0.8320 (t0) cc_final: 0.8064 (m-40) outliers start: 14 outliers final: 11 residues processed: 140 average time/residue: 0.1062 time to fit residues: 22.0255 Evaluate side-chains 139 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.196879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156806 restraints weight = 14109.992| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.75 r_work: 0.3754 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11762 Z= 0.115 Angle : 0.556 9.064 15928 Z= 0.283 Chirality : 0.040 0.187 1754 Planarity : 0.003 0.030 1998 Dihedral : 3.889 15.660 1546 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.12 % Allowed : 14.34 % Favored : 84.54 % 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: 0.75 (0.23), residues: 1382 helix: 1.88 (0.18), residues: 854 sheet: -2.90 (0.63), residues: 58 loop : -1.72 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.011 0.001 TYR A 687 PHE 0.029 0.001 PHE A 126 TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11754) covalent geometry : angle 0.55354 / 0.28 (15912) SS BOND : bond 0.00249 / 0.11 ( 8) SS BOND : angle 1.61075 / 0.87 ( 16) hydrogen bonds : bond 0.03529 / 2.25 ( 661) hydrogen bonds : angle 3.81573 / 2.63 ( 1947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.447 Fit side-chains REVERT: A 175 LYS cc_start: 0.8033 (tptm) cc_final: 0.7410 (ttpp) REVERT: A 176 MET cc_start: 0.5931 (ttt) cc_final: 0.5697 (ttt) REVERT: A 909 MET cc_start: 0.4787 (ttm) cc_final: 0.3648 (tpt) REVERT: B 730 ASN cc_start: 0.8256 (t0) cc_final: 0.8027 (m-40) outliers start: 14 outliers final: 12 residues processed: 138 average time/residue: 0.1043 time to fit residues: 21.3364 Evaluate side-chains 139 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.192300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152495 restraints weight = 14297.825| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.85 r_work: 0.3668 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11762 Z= 0.182 Angle : 0.623 9.460 15928 Z= 0.322 Chirality : 0.042 0.171 1754 Planarity : 0.004 0.030 1998 Dihedral : 4.102 17.498 1546 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.36 % Allowed : 14.18 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1382 helix: 1.56 (0.17), residues: 860 sheet: -2.99 (0.63), residues: 58 loop : -1.90 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 748 TYR 0.015 0.002 TYR B 838 PHE 0.027 0.002 PHE A 126 TRP 0.012 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (11754) covalent geometry : angle 0.62097 / 0.32 (15912) SS BOND : bond 0.00195 / 0.09 ( 8) SS BOND : angle 1.87561 / 1.00 ( 16) hydrogen bonds : bond 0.04087 / 2.62 ( 661) hydrogen bonds : angle 4.02626 / 2.79 ( 1947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.452 Fit side-chains REVERT: A 175 LYS cc_start: 0.8103 (tptm) cc_final: 0.7485 (ttpp) REVERT: A 176 MET cc_start: 0.6083 (ttt) cc_final: 0.5812 (ttt) REVERT: A 752 ILE cc_start: 0.8484 (tt) cc_final: 0.7923 (mm) REVERT: B 730 ASN cc_start: 0.8433 (t0) cc_final: 0.8123 (m-40) outliers start: 17 outliers final: 16 residues processed: 142 average time/residue: 0.1022 time to fit residues: 21.4707 Evaluate side-chains 142 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.193722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.154321 restraints weight = 14241.122| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.94 r_work: 0.3680 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11762 Z= 0.147 Angle : 0.594 9.268 15928 Z= 0.305 Chirality : 0.041 0.215 1754 Planarity : 0.003 0.031 1998 Dihedral : 4.057 16.736 1546 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.52 % Allowed : 14.10 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1382 helix: 1.62 (0.17), residues: 860 sheet: -3.06 (0.61), residues: 58 loop : -1.88 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.012 0.001 TYR B 838 PHE 0.027 0.001 PHE A 126 TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11754) covalent geometry : angle 0.59138 / 0.30 (15912) SS BOND : bond 0.00219 / 0.10 ( 8) SS BOND : angle 1.79983 / 0.96 ( 16) hydrogen bonds : bond 0.03856 / 2.46 ( 661) hydrogen bonds : angle 3.96896 / 2.74 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3213.10 seconds wall clock time: 55 minutes 53.00 seconds (3353.00 seconds total)