Starting phenix.real_space_refine on Sun Sep 13 07:28:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rom_54124/09_2026/9rom_54124_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rom_54124/09_2026/9rom_54124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rom_54124/09_2026/9rom_54124_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rom_54124/09_2026/9rom_54124_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rom_54124/09_2026/9rom_54124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rom_54124/09_2026/9rom_54124.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 61 5.16 5 C 6667 2.51 5 N 1718 2.21 5 O 1952 1.98 5 H 10290 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20689 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 15431 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 953} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4621 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Chain: "C" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 511 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.18 Number of scatterers: 20689 At special positions: 0 Unit cell: (87.502, 90.114, 177.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 1 15.00 O 1952 8.00 N 1718 7.00 C 6667 6.00 H 10290 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " " NAG B 402 " - " ASN B 193 " " NAG B 403 " - " ASN B 265 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 607.7 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 48.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.663A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.509A pdb=" N CYS A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 4.341A pdb=" N LEU A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 118 through 151 removed outlier: 4.069A pdb=" N PHE A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.683A pdb=" N VAL A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.685A pdb=" N ALA A 353 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 354 " --> pdb=" O LEU A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 354' Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.873A pdb=" N ALA A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 746 through 772 removed outlier: 3.917A pdb=" N THR A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 803 Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.503A pdb=" N ILE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 836 through 846 removed outlier: 3.885A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 867 Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.638A pdb=" N LEU A 873 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 928 removed outlier: 3.761A pdb=" N ARG A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 962 through 966 removed outlier: 3.761A pdb=" N ASP A 965 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 966 " --> pdb=" O GLY A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 962 through 966' Processing helix chain 'A' and resid 974 through 979 removed outlier: 4.025A pdb=" N TRP A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 979 " --> pdb=" O PRO A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 979' Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 removed outlier: 3.580A pdb=" N LYS A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 59 removed outlier: 3.906A pdb=" N PHE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.674A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 removed outlier: 3.650A pdb=" N LEU C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 56 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 11.681A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 242 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 200 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 244 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 198 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 246 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE A 196 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 250 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 4.009A pdb=" N ASP A 187 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 242 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 200 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 244 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 198 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 246 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE A 196 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 250 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 233 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.706A pdb=" N LEU A 740 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 7.235A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU A 484 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 466 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 7.235A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU A 573 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 577 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 605 through 606 removed outlier: 6.256A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS A 653 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA A 681 " --> pdb=" O CYS A 653 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB1, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.506A pdb=" N ILE B 299 " --> pdb=" O ILE B 272 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1440 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: 5.41 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10265 1.03 - 1.23: 136 1.23 - 1.43: 4196 1.43 - 1.62: 6218 1.62 - 1.82: 91 Bond restraints: 20906 Sorted by residual: bond pdb=" C PHD A 366 " pdb=" O PHD A 366 " ideal model delta sigma weight residual 1.231 1.267 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 1.816 1.780 0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA PHD A 366 " pdb=" C PHD A 366 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.10e-02 2.27e+03 2.60e+00 bond pdb=" CG PHD A 366 " pdb=" OD2 PHD A 366 " ideal model delta sigma weight residual 1.218 1.249 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 ... (remaining 20901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.29: 37821 7.29 - 14.58: 6 14.58 - 21.87: 0 21.87 - 29.17: 1 29.17 - 36.46: 20 Bond angle restraints: 37848 Sorted by residual: angle pdb=" C LYS B 302 " pdb=" CA LYS B 302 " pdb=" HA LYS B 302 " ideal model delta sigma weight residual 109.00 72.54 36.46 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C THR B 166 " pdb=" CA THR B 166 " pdb=" HA THR B 166 " ideal model delta sigma weight residual 109.00 72.72 36.28 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C TYR B 167 " pdb=" CA TYR B 167 " pdb=" HA TYR B 167 " ideal model delta sigma weight residual 109.00 73.22 35.78 3.00e+00 1.11e-01 1.42e+02 angle pdb=" N GLU B 300 " pdb=" CA GLU B 300 " pdb=" HA GLU B 300 " ideal model delta sigma weight residual 110.00 74.23 35.77 3.00e+00 1.11e-01 1.42e+02 angle pdb=" N LYS B 302 " pdb=" CA LYS B 302 " pdb=" HA LYS B 302 " ideal model delta sigma weight residual 110.00 74.28 35.72 3.00e+00 1.11e-01 1.42e+02 ... (remaining 37843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8795 17.94 - 35.88: 846 35.88 - 53.82: 280 53.82 - 71.77: 71 71.77 - 89.71: 22 Dihedral angle restraints: 10014 sinusoidal: 5624 harmonic: 4390 Sorted by residual: dihedral pdb=" CA TYR B 167 " pdb=" C TYR B 167 " pdb=" N GLY B 168 " pdb=" CA GLY B 168 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LYS B 221 " pdb=" C LYS B 221 " pdb=" N ASP B 222 " pdb=" CA ASP B 222 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C TYR B 167 " pdb=" N TYR B 167 " pdb=" CA TYR B 167 " pdb=" CB TYR B 167 " ideal model delta harmonic sigma weight residual -122.60 -134.15 11.55 0 2.50e+00 1.60e-01 2.14e+01 ... (remaining 10011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1563 0.095 - 0.190: 76 0.190 - 0.285: 0 0.285 - 0.380: 1 0.380 - 0.475: 6 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CA SER B 303 " pdb=" N SER B 303 " pdb=" C SER B 303 " pdb=" CB SER B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CA LYS B 22 " pdb=" N LYS B 22 " pdb=" C LYS B 22 " pdb=" CB LYS B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA TYR B 167 " pdb=" N TYR B 167 " pdb=" C TYR B 167 " pdb=" CB TYR B 167 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 1643 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 167 " 0.022 2.00e-02 2.50e+03 1.04e-02 3.26e+00 pdb=" CG TYR B 167 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 167 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 167 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 167 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 167 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 167 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 167 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR B 167 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 167 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR B 167 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR B 167 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 887 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ASP A 887 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP A 887 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 888 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 992 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" CG ASP A 992 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 992 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 992 " 0.010 2.00e-02 2.50e+03 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1099 2.16 - 2.77: 41185 2.77 - 3.38: 60043 3.38 - 3.99: 75362 3.99 - 4.60: 116458 Nonbonded interactions: 294147 Sorted by model distance: nonbonded pdb=" O ALA A 379 " pdb=" H ALA A 390 " model vdw 1.547 2.450 nonbonded pdb=" H ASN A 828 " pdb=" OD2 ASP A 832 " model vdw 1.567 2.450 nonbonded pdb=" H LYS B 22 " pdb=" HA LYS B 22 " model vdw 1.591 1.816 nonbonded pdb=" O GLN A 157 " pdb=" H ALA A 172 " model vdw 1.592 2.450 nonbonded pdb=" OE1 GLU B 287 " pdb=" H GLU B 287 " model vdw 1.598 2.450 ... (remaining 294142 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.140 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.760 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 0.036 10622 Z= 0.175 Angle : 0.611 10.488 14418 Z= 0.310 Chirality : 0.049 0.475 1646 Planarity : 0.004 0.039 1837 Dihedral : 16.185 89.708 4151 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.14 % Favored : 93.78 % Rotamer: Outliers : 0.80 % Allowed : 20.25 % Favored : 78.95 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % 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 (0.24), residues: 1303 helix: 1.04 (0.22), residues: 570 sheet: -0.83 (0.49), residues: 121 loop : -1.13 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 995 TYR 0.028 0.001 TYR B 167 PHE 0.013 0.001 PHE B 90 TRP 0.006 0.001 TRP A 921 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (10616) covalent geometry : angle 0.61038 / 0.31 (14403) SS BOND : bond 0.00266 / 0.13 ( 3) SS BOND : angle 0.61075 / 0.32 ( 6) hydrogen bonds : bond 0.14311 / 9.91 ( 497) hydrogen bonds : angle 6.25602 / 4.58 ( 1440) link_NAG-ASN : bond 0.00219 / 0.11 ( 3) link_NAG-ASN : angle 1.50483 / 1.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.4914 (tpt) cc_final: 0.4308 (ttt) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.1776 time to fit residues: 22.3602 Evaluate side-chains 73 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 129 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN B 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.143609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101226 restraints weight = 82539.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103441 restraints weight = 33855.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.104232 restraints weight = 22645.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104740 restraints weight = 22037.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104631 restraints weight = 17103.079| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10622 Z= 0.139 Angle : 0.567 10.888 14418 Z= 0.295 Chirality : 0.049 0.471 1646 Planarity : 0.004 0.040 1837 Dihedral : 6.479 52.744 1688 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 0.89 % Allowed : 20.25 % Favored : 78.86 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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: 0.07 (0.23), residues: 1303 helix: 1.37 (0.22), residues: 575 sheet: -0.85 (0.48), residues: 120 loop : -1.07 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 901 TYR 0.023 0.001 TYR B 167 PHE 0.018 0.001 PHE B 90 TRP 0.004 0.001 TRP A1006 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (10616) covalent geometry : angle 0.56520 / 0.29 (14403) SS BOND : bond 0.00188 / 0.09 ( 3) SS BOND : angle 0.49016 / 0.26 ( 6) hydrogen bonds : bond 0.04521 / 3.13 ( 497) hydrogen bonds : angle 4.89310 / 3.67 ( 1440) link_NAG-ASN : bond 0.00240 / 0.12 ( 3) link_NAG-ASN : angle 1.75711 / 1.27 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7507 (tmm) cc_final: 0.7279 (tmm) REVERT: A 265 SER cc_start: 0.8537 (t) cc_final: 0.8049 (p) REVERT: A 724 MET cc_start: 0.8854 (mmp) cc_final: 0.8642 (mmp) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.1826 time to fit residues: 26.4832 Evaluate side-chains 75 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 127 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.141756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096759 restraints weight = 81539.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.100746 restraints weight = 32609.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103119 restraints weight = 19778.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104424 restraints weight = 15123.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105028 restraints weight = 13145.413| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10622 Z= 0.219 Angle : 0.588 9.808 14418 Z= 0.309 Chirality : 0.050 0.472 1646 Planarity : 0.004 0.044 1837 Dihedral : 6.538 53.330 1683 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 2.22 % Allowed : 19.98 % Favored : 77.80 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.13 (0.23), residues: 1303 helix: 1.25 (0.21), residues: 584 sheet: -0.91 (0.48), residues: 120 loop : -1.26 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 901 TYR 0.025 0.002 TYR B 167 PHE 0.013 0.001 PHE B 90 TRP 0.005 0.001 TRP A1006 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (10616) covalent geometry : angle 0.58550 / 0.31 (14403) SS BOND : bond 0.00299 / 0.15 ( 3) SS BOND : angle 0.56454 / 0.30 ( 6) hydrogen bonds : bond 0.04257 / 2.92 ( 497) hydrogen bonds : angle 4.83490 / 3.63 ( 1440) link_NAG-ASN : bond 0.00359 / 0.18 ( 3) link_NAG-ASN : angle 2.04992 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8083 (mpp) cc_final: 0.7785 (mpp) REVERT: A 229 THR cc_start: 0.4835 (OUTLIER) cc_final: 0.4568 (t) REVERT: A 265 SER cc_start: 0.8674 (t) cc_final: 0.8283 (p) REVERT: A 324 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7593 (mp0) outliers start: 25 outliers final: 16 residues processed: 92 average time/residue: 0.1564 time to fit residues: 23.4248 Evaluate side-chains 85 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 40.0000 chunk 128 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 120 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.142856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100465 restraints weight = 81480.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.102696 restraints weight = 34020.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102843 restraints weight = 22539.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103590 restraints weight = 22367.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103459 restraints weight = 17785.801| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10622 Z= 0.148 Angle : 0.553 10.283 14418 Z= 0.285 Chirality : 0.049 0.471 1646 Planarity : 0.004 0.044 1837 Dihedral : 6.334 53.295 1683 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 2.22 % Allowed : 20.16 % Favored : 77.62 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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: 0.06 (0.23), residues: 1303 helix: 1.44 (0.21), residues: 585 sheet: -0.89 (0.49), residues: 120 loop : -1.19 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.023 0.001 TYR B 167 PHE 0.016 0.001 PHE B 90 TRP 0.005 0.001 TRP A1006 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10616) covalent geometry : angle 0.55145 / 0.28 (14403) SS BOND : bond 0.00185 / 0.09 ( 3) SS BOND : angle 0.49636 / 0.26 ( 6) hydrogen bonds : bond 0.03879 / 2.65 ( 497) hydrogen bonds : angle 4.57616 / 3.44 ( 1440) link_NAG-ASN : bond 0.00205 / 0.10 ( 3) link_NAG-ASN : angle 1.82685 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8128 (mpp) cc_final: 0.7864 (mpp) REVERT: A 229 THR cc_start: 0.5567 (OUTLIER) cc_final: 0.5352 (t) REVERT: A 265 SER cc_start: 0.8582 (t) cc_final: 0.8164 (p) REVERT: A 946 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8844 (t80) outliers start: 25 outliers final: 19 residues processed: 96 average time/residue: 0.1667 time to fit residues: 26.1476 Evaluate side-chains 88 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 14 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.142826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099818 restraints weight = 82316.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.102220 restraints weight = 34465.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102404 restraints weight = 22896.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103140 restraints weight = 22429.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102971 restraints weight = 17958.817| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10622 Z= 0.151 Angle : 0.554 10.215 14418 Z= 0.285 Chirality : 0.049 0.471 1646 Planarity : 0.004 0.045 1837 Dihedral : 6.298 57.621 1683 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 2.22 % Allowed : 19.98 % Favored : 77.80 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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: 0.16 (0.23), residues: 1303 helix: 1.54 (0.21), residues: 586 sheet: -0.84 (0.49), residues: 120 loop : -1.17 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.023 0.001 TYR B 167 PHE 0.016 0.001 PHE B 90 TRP 0.005 0.001 TRP A1006 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10616) covalent geometry : angle 0.55215 / 0.28 (14403) SS BOND : bond 0.00193 / 0.09 ( 3) SS BOND : angle 0.48373 / 0.26 ( 6) hydrogen bonds : bond 0.03736 / 2.53 ( 497) hydrogen bonds : angle 4.48668 / 3.37 ( 1440) link_NAG-ASN : bond 0.00247 / 0.12 ( 3) link_NAG-ASN : angle 1.81438 / 1.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8048 (mpp) cc_final: 0.7759 (mpp) REVERT: A 265 SER cc_start: 0.8576 (t) cc_final: 0.8150 (p) REVERT: A 324 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 381 MET cc_start: 0.2639 (mmt) cc_final: 0.1820 (mpp) REVERT: A 946 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8819 (t80) REVERT: A 970 MET cc_start: 0.8749 (mmt) cc_final: 0.8080 (mtt) outliers start: 25 outliers final: 22 residues processed: 94 average time/residue: 0.1578 time to fit residues: 23.6832 Evaluate side-chains 90 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.142278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099766 restraints weight = 83975.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102951 restraints weight = 35154.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102661 restraints weight = 22454.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103682 restraints weight = 22601.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103455 restraints weight = 18019.179| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10622 Z= 0.138 Angle : 0.542 10.263 14418 Z= 0.279 Chirality : 0.049 0.469 1646 Planarity : 0.003 0.045 1837 Dihedral : 6.264 55.169 1683 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.58 % Allowed : 20.16 % Favored : 77.26 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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: 0.24 (0.23), residues: 1303 helix: 1.61 (0.21), residues: 587 sheet: -0.80 (0.50), residues: 120 loop : -1.13 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.021 0.001 TYR B 167 PHE 0.015 0.001 PHE B 90 TRP 0.005 0.001 TRP A1006 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10616) covalent geometry : angle 0.54017 / 0.28 (14403) SS BOND : bond 0.00155 / 0.08 ( 3) SS BOND : angle 0.47078 / 0.25 ( 6) hydrogen bonds : bond 0.03636 / 2.45 ( 497) hydrogen bonds : angle 4.41576 / 3.32 ( 1440) link_NAG-ASN : bond 0.00215 / 0.11 ( 3) link_NAG-ASN : angle 1.73119 / 1.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.4983 (tpt) cc_final: 0.4372 (ttt) REVERT: A 168 MET cc_start: 0.8131 (mpp) cc_final: 0.7832 (mpp) REVERT: A 265 SER cc_start: 0.8613 (t) cc_final: 0.8191 (p) REVERT: A 381 MET cc_start: 0.2601 (mmt) cc_final: 0.1782 (mpp) REVERT: A 670 GLU cc_start: 0.8601 (pp20) cc_final: 0.8262 (pp20) REVERT: A 738 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7418 (tpp) REVERT: A 812 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 946 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8809 (t80) REVERT: A 970 MET cc_start: 0.8741 (mmt) cc_final: 0.8085 (mtt) outliers start: 29 outliers final: 22 residues processed: 95 average time/residue: 0.1669 time to fit residues: 25.6297 Evaluate side-chains 90 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.142312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100107 restraints weight = 83939.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102635 restraints weight = 36637.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102794 restraints weight = 24079.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103646 restraints weight = 24005.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.103431 restraints weight = 19019.968| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10622 Z= 0.139 Angle : 0.541 10.220 14418 Z= 0.279 Chirality : 0.049 0.469 1646 Planarity : 0.003 0.045 1837 Dihedral : 6.205 53.269 1683 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.49 % Allowed : 19.98 % Favored : 77.53 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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: 0.30 (0.23), residues: 1303 helix: 1.69 (0.21), residues: 587 sheet: -0.80 (0.49), residues: 120 loop : -1.13 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.022 0.001 TYR B 167 PHE 0.015 0.001 PHE B 90 TRP 0.005 0.001 TRP A1006 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10616) covalent geometry : angle 0.53959 / 0.28 (14403) SS BOND : bond 0.00175 / 0.09 ( 3) SS BOND : angle 0.46868 / 0.25 ( 6) hydrogen bonds : bond 0.03532 / 2.38 ( 497) hydrogen bonds : angle 4.35060 / 3.27 ( 1440) link_NAG-ASN : bond 0.00225 / 0.11 ( 3) link_NAG-ASN : angle 1.74202 / 1.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.4942 (tpt) cc_final: 0.4344 (ttt) REVERT: A 168 MET cc_start: 0.8161 (mpp) cc_final: 0.7862 (mpp) REVERT: A 265 SER cc_start: 0.8610 (t) cc_final: 0.8177 (p) REVERT: A 381 MET cc_start: 0.2610 (mmt) cc_final: 0.1862 (mpp) REVERT: A 812 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8674 (mp) REVERT: A 946 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8791 (t80) REVERT: A 970 MET cc_start: 0.8772 (mmt) cc_final: 0.8092 (mtt) outliers start: 28 outliers final: 23 residues processed: 94 average time/residue: 0.1650 time to fit residues: 25.1614 Evaluate side-chains 93 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.0370 chunk 37 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.140982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.098536 restraints weight = 83243.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101175 restraints weight = 34890.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101049 restraints weight = 23160.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.102013 restraints weight = 23170.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101818 restraints weight = 18281.957| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10622 Z= 0.210 Angle : 0.575 9.557 14418 Z= 0.300 Chirality : 0.050 0.470 1646 Planarity : 0.004 0.045 1837 Dihedral : 6.368 53.740 1683 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.40 % Allowed : 19.80 % Favored : 77.80 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.15 (0.23), residues: 1303 helix: 1.57 (0.21), residues: 587 sheet: -0.88 (0.49), residues: 120 loop : -1.20 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.024 0.001 TYR B 167 PHE 0.014 0.001 PHE B 90 TRP 0.006 0.001 TRP A1006 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (10616) covalent geometry : angle 0.57278 / 0.30 (14403) SS BOND : bond 0.00281 / 0.14 ( 3) SS BOND : angle 0.50210 / 0.27 ( 6) hydrogen bonds : bond 0.03698 / 2.49 ( 497) hydrogen bonds : angle 4.47968 / 3.36 ( 1440) link_NAG-ASN : bond 0.00371 / 0.19 ( 3) link_NAG-ASN : angle 1.90799 / 1.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.4951 (tpt) cc_final: 0.4289 (ttt) REVERT: A 168 MET cc_start: 0.8182 (mpp) cc_final: 0.7869 (mpp) REVERT: A 265 SER cc_start: 0.8661 (t) cc_final: 0.8235 (p) REVERT: A 946 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8810 (t80) outliers start: 27 outliers final: 25 residues processed: 88 average time/residue: 0.1673 time to fit residues: 24.3145 Evaluate side-chains 90 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.142740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100666 restraints weight = 84547.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103213 restraints weight = 36466.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103363 restraints weight = 24174.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104199 restraints weight = 23761.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104037 restraints weight = 19028.893| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10622 Z= 0.107 Angle : 0.536 10.433 14418 Z= 0.275 Chirality : 0.049 0.464 1646 Planarity : 0.003 0.045 1837 Dihedral : 6.147 53.925 1683 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.13 % Allowed : 20.16 % Favored : 77.71 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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: 0.40 (0.24), residues: 1303 helix: 1.79 (0.21), residues: 588 sheet: -0.87 (0.49), residues: 120 loop : -1.08 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.019 0.001 TYR B 167 PHE 0.017 0.001 PHE B 90 TRP 0.005 0.001 TRP A1006 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10616) covalent geometry : angle 0.53452 / 0.27 (14403) SS BOND : bond 0.00112 / 0.06 ( 3) SS BOND : angle 0.51415 / 0.27 ( 6) hydrogen bonds : bond 0.03435 / 2.31 ( 497) hydrogen bonds : angle 4.21094 / 3.17 ( 1440) link_NAG-ASN : bond 0.00143 / 0.07 ( 3) link_NAG-ASN : angle 1.71777 / 1.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.4893 (tpt) cc_final: 0.4242 (ttt) REVERT: A 168 MET cc_start: 0.8140 (mpp) cc_final: 0.7850 (mpp) REVERT: A 265 SER cc_start: 0.8687 (t) cc_final: 0.8326 (p) REVERT: A 670 GLU cc_start: 0.8711 (pp20) cc_final: 0.8341 (pp20) REVERT: A 946 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8749 (t80) REVERT: A 970 MET cc_start: 0.8756 (mmt) cc_final: 0.8049 (mtt) outliers start: 24 outliers final: 22 residues processed: 97 average time/residue: 0.1676 time to fit residues: 26.6781 Evaluate side-chains 96 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.141616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.096798 restraints weight = 84801.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101097 restraints weight = 32588.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103698 restraints weight = 19394.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105001 restraints weight = 14644.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105840 restraints weight = 12681.281| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10622 Z= 0.172 Angle : 0.561 9.862 14418 Z= 0.290 Chirality : 0.049 0.469 1646 Planarity : 0.004 0.046 1837 Dihedral : 6.245 53.729 1683 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.13 % Allowed : 20.43 % Favored : 77.44 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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 (0.23), residues: 1303 helix: 1.73 (0.21), residues: 588 sheet: -0.84 (0.49), residues: 120 loop : -1.14 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.022 0.001 TYR B 167 PHE 0.014 0.001 PHE B 90 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (10616) covalent geometry : angle 0.55911 / 0.29 (14403) SS BOND : bond 0.00233 / 0.11 ( 3) SS BOND : angle 0.49106 / 0.26 ( 6) hydrogen bonds : bond 0.03517 / 2.36 ( 497) hydrogen bonds : angle 4.31718 / 3.24 ( 1440) link_NAG-ASN : bond 0.00317 / 0.16 ( 3) link_NAG-ASN : angle 1.79017 / 1.14 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.5077 (tpt) cc_final: 0.4467 (ttt) REVERT: A 168 MET cc_start: 0.7854 (mpp) cc_final: 0.7514 (mpp) REVERT: A 265 SER cc_start: 0.8787 (t) cc_final: 0.8390 (p) REVERT: A 376 MET cc_start: 0.5120 (mtt) cc_final: 0.4865 (mtm) REVERT: A 946 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8762 (t80) outliers start: 24 outliers final: 23 residues processed: 89 average time/residue: 0.1671 time to fit residues: 24.3422 Evaluate side-chains 90 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 20.0000 chunk 87 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.141911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099777 restraints weight = 84735.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102350 restraints weight = 36022.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102340 restraints weight = 24679.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103229 restraints weight = 24499.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103015 restraints weight = 19399.914| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10622 Z= 0.146 Angle : 0.547 9.994 14418 Z= 0.281 Chirality : 0.049 0.467 1646 Planarity : 0.004 0.046 1837 Dihedral : 6.217 54.512 1683 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.22 % Allowed : 20.34 % Favored : 77.44 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.61 % 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: 0.35 (0.23), residues: 1303 helix: 1.75 (0.21), residues: 588 sheet: -0.83 (0.49), residues: 120 loop : -1.12 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.020 0.001 TYR B 167 PHE 0.015 0.001 PHE B 90 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (10616) covalent geometry : angle 0.54549 / 0.28 (14403) SS BOND : bond 0.00206 / 0.10 ( 3) SS BOND : angle 0.51014 / 0.27 ( 6) hydrogen bonds : bond 0.03463 / 2.33 ( 497) hydrogen bonds : angle 4.25416 / 3.20 ( 1440) link_NAG-ASN : bond 0.00222 / 0.11 ( 3) link_NAG-ASN : angle 1.75959 / 1.16 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.98 seconds wall clock time: 58 minutes 13.55 seconds (3493.55 seconds total)