Starting phenix.real_space_refine on Wed Mar 4 05:24:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e20_30948/03_2026/7e20_30948_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e20_30948/03_2026/7e20_30948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e20_30948/03_2026/7e20_30948_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e20_30948/03_2026/7e20_30948_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e20_30948/03_2026/7e20_30948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e20_30948/03_2026/7e20_30948.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 6906 2.51 5 N 1741 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10694 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7712 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 43, 'TRANS': 950} Chain: "B" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2404 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 273} Chain: "C" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Unusual residues: {' K': 3, ' MG': 1, 'PC1': 1, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'NAG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.25 Number of scatterers: 10694 At special positions: 0 Unit cell: (100.004, 94.569, 185.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 3 19.00 S 58 16.00 P 1 15.00 Mg 1 11.99 O 1984 8.00 N 1741 7.00 C 6906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 249 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 584 " distance=2.01 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.18 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 BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 403 " - " ASN B 265 " " NAG D 1 " - " ASN B 158 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 513.1 milliseconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 48.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.665A pdb=" N ARG A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.972A pdb=" N GLU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 95 through 98 removed outlier: 3.868A pdb=" N GLY A 98 " --> pdb=" O GLN A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 99 through 120 removed outlier: 4.227A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 removed outlier: 3.780A pdb=" N TYR A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.990A pdb=" N SER A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.886A pdb=" N VAL A 185 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 306 removed outlier: 3.739A pdb=" N HIS A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 316 through 330 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.656A pdb=" N ARG A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 4.040A pdb=" N THR A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 367' Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.742A pdb=" N LEU A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.554A pdb=" N LYS A 444 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 4.115A pdb=" N LEU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.570A pdb=" N LYS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.680A pdb=" N GLY A 604 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.875A pdb=" N VAL A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.694A pdb=" N LYS A 671 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 667 through 672' Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.624A pdb=" N ASP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 708 removed outlier: 4.077A pdb=" N LEU A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 755 through 782 removed outlier: 4.224A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 770 " --> pdb=" O ARG A 766 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 773 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Proline residue: A 789 - end of helix removed outlier: 3.632A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 812 removed outlier: 3.612A pdb=" N ILE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 811 " --> pdb=" O ILE A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 821 Processing helix chain 'A' and resid 822 through 825 Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.557A pdb=" N ARG A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 removed outlier: 3.633A pdb=" N GLN A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 removed outlier: 3.725A pdb=" N ILE A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 873 " --> pdb=" O TYR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 937 removed outlier: 3.763A pdb=" N ILE A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.581A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 removed outlier: 3.606A pdb=" N ALA A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.584A pdb=" N TRP A 988 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 989 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 990 " --> pdb=" O TRP A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 Processing helix chain 'A' and resid 1015 through 1022 removed outlier: 3.648A pdb=" N TYR A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 59 removed outlier: 3.994A pdb=" N ILE B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.846A pdb=" N VAL B 72 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.559A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.556A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.892A pdb=" N GLY B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'C' and resid 22 through 46 removed outlier: 4.321A pdb=" N VAL C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.552A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 227 removed outlier: 4.144A pdb=" N CYS A 211 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.450A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 715 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 398 through 399 removed outlier: 6.791A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.120A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 437 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1774 1.31 - 1.44: 2749 1.44 - 1.57: 6260 1.57 - 1.70: 56 1.70 - 1.83: 86 Bond restraints: 10925 Sorted by residual: bond pdb=" CAI Y01 C1501 " pdb=" CAZ Y01 C1501 " ideal model delta sigma weight residual 1.332 1.555 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAI Y01 B 401 " pdb=" CAZ Y01 B 401 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CAI Y01 A1105 " pdb=" CAZ Y01 A1105 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAI Y01 B 402 " pdb=" CAZ Y01 B 402 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAI Y01 A1107 " pdb=" CAZ Y01 A1107 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 10920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 14711 5.61 - 11.22: 98 11.22 - 16.82: 10 16.82 - 22.43: 0 22.43 - 28.04: 7 Bond angle restraints: 14826 Sorted by residual: angle pdb=" CAD Y01 B 401 " pdb=" CBH Y01 B 401 " pdb=" CBF Y01 B 401 " ideal model delta sigma weight residual 111.82 83.78 28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" CAD Y01 B 402 " pdb=" CBH Y01 B 402 " pdb=" CBF Y01 B 402 " ideal model delta sigma weight residual 111.82 84.17 27.65 3.00e+00 1.11e-01 8.50e+01 angle pdb=" CAD Y01 B 401 " pdb=" CBH Y01 B 401 " pdb=" CAT Y01 B 401 " ideal model delta sigma weight residual 109.59 83.48 26.11 3.00e+00 1.11e-01 7.58e+01 angle pdb=" CAD Y01 B 402 " pdb=" CBH Y01 B 402 " pdb=" CAT Y01 B 402 " ideal model delta sigma weight residual 109.59 83.54 26.05 3.00e+00 1.11e-01 7.54e+01 angle pdb=" CAD Y01 B 402 " pdb=" CBH Y01 B 402 " pdb=" CAZ Y01 B 402 " ideal model delta sigma weight residual 108.53 83.14 25.39 3.00e+00 1.11e-01 7.16e+01 ... (remaining 14821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6550 35.66 - 71.33: 217 71.33 - 106.99: 54 106.99 - 142.65: 98 142.65 - 178.31: 13 Dihedral angle restraints: 6932 sinusoidal: 3126 harmonic: 3806 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS A 249 " pdb=" CB CYS A 249 " ideal model delta sinusoidal sigma weight residual -86.00 -166.31 80.31 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA ALA A 152 " pdb=" C ALA A 152 " pdb=" N LYS A 153 " pdb=" CA LYS A 153 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR B 242 " pdb=" C TYR B 242 " pdb=" N TYR B 243 " pdb=" CA TYR B 243 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 6929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.200: 1651 1.200 - 2.400: 0 2.400 - 3.601: 0 3.601 - 4.801: 2 4.801 - 6.001: 28 Chirality restraints: 1681 Sorted by residual: chirality pdb=" CBI Y01 A1105 " pdb=" CAU Y01 A1105 " pdb=" CBE Y01 A1105 " pdb=" CBG Y01 A1105 " both_signs ideal model delta sigma weight residual False 2.94 -3.06 6.00 2.00e-01 2.50e+01 9.00e+02 chirality pdb=" CBI Y01 C1501 " pdb=" CAU Y01 C1501 " pdb=" CBE Y01 C1501 " pdb=" CBG Y01 C1501 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.99 2.00e-01 2.50e+01 8.97e+02 chirality pdb=" CBI Y01 B 402 " pdb=" CAU Y01 B 402 " pdb=" CBE Y01 B 402 " pdb=" CBG Y01 B 402 " both_signs ideal model delta sigma weight residual False 2.94 -3.04 5.98 2.00e-01 2.50e+01 8.94e+02 ... (remaining 1678 not shown) Planarity restraints: 1871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 199 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO B 200 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 788 " -0.047 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A 789 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 789 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 789 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 132 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO B 133 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.034 5.00e-02 4.00e+02 ... (remaining 1868 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.73: 654 2.73 - 3.33: 11381 3.33 - 3.93: 19777 3.93 - 4.54: 27329 4.54 - 5.14: 42493 Nonbonded interactions: 101634 Sorted by model distance: nonbonded pdb=" O THR A 378 " pdb="MG MG A1104 " model vdw 2.127 2.170 nonbonded pdb=" CAP Y01 A1107 " pdb=" CAC Y01 B 402 " model vdw 2.204 3.860 nonbonded pdb=" OD1 ASP A 717 " pdb="MG MG A1104 " model vdw 2.208 2.170 nonbonded pdb=" CD1 ILE A 881 " pdb=" OAG Y01 A1107 " model vdw 2.218 3.460 nonbonded pdb=" SD MET A 859 " pdb=" CAA Y01 A1107 " model vdw 2.272 3.820 ... (remaining 101629 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.012 0.223 10933 Z= 0.589 Angle : 1.373 36.714 14845 Z= 0.644 Chirality : 0.716 6.001 1681 Planarity : 0.008 0.077 1869 Dihedral : 27.528 178.312 4473 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.77 % Favored : 92.70 % Rotamer: Outliers : 1.15 % Allowed : 6.61 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -3.51 (0.19), residues: 1315 helix: -2.52 (0.16), residues: 559 sheet: -0.95 (0.36), residues: 162 loop : -2.45 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 227 TYR 0.040 0.002 TYR B 243 PHE 0.040 0.003 PHE A 291 TRP 0.024 0.003 TRP A 392 HIS 0.005 0.002 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.01229 (10925) covalent geometry : angle 1.32834 (14826) SS BOND : bond 0.06866 ( 5) SS BOND : angle 13.00392 ( 10) hydrogen bonds : bond 0.17697 ( 437) hydrogen bonds : angle 6.58020 ( 1242) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 3.37254 ( 3) link_NAG-ASN : bond 0.00463 ( 2) link_NAG-ASN : angle 4.01343 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8164 (mt) cc_final: 0.7882 (tm) REVERT: A 211 CYS cc_start: 0.5266 (OUTLIER) cc_final: 0.4868 (p) REVERT: A 423 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7627 (ptp90) REVERT: A 507 MET cc_start: 0.7515 (ptt) cc_final: 0.7120 (pp-130) REVERT: A 593 ASP cc_start: 0.8101 (t0) cc_final: 0.7889 (t70) REVERT: A 654 GLN cc_start: 0.7626 (mt0) cc_final: 0.7284 (mt0) REVERT: A 847 GLU cc_start: 0.7507 (pm20) cc_final: 0.7207 (pm20) REVERT: B 17 TRP cc_start: 0.6202 (t-100) cc_final: 0.5909 (t60) outliers start: 13 outliers final: 1 residues processed: 166 average time/residue: 0.7112 time to fit residues: 125.4871 Evaluate side-chains 103 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 225 GLN A 398 HIS A 436 ASN A 437 GLN A 524 HIS A 539 GLN A 540 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 656 ASN A 797 ASN A 882 HIS A 905 GLN B 55 GLN B 104 ASN B 141 HIS B 163 ASN B 282 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.145472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113336 restraints weight = 16491.406| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.05 r_work: 0.3275 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10933 Z= 0.133 Angle : 1.499 34.133 14845 Z= 0.557 Chirality : 0.144 1.855 1681 Planarity : 0.006 0.056 1869 Dihedral : 29.417 179.523 1964 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.94 % Allowed : 12.25 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.22), residues: 1315 helix: -0.66 (0.21), residues: 560 sheet: -0.44 (0.39), residues: 151 loop : -1.92 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.029 0.001 TYR B 243 PHE 0.019 0.001 PHE A 291 TRP 0.015 0.001 TRP A 392 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00291 (10925) covalent geometry : angle 1.49684 (14826) SS BOND : bond 0.01092 ( 5) SS BOND : angle 2.37223 ( 10) hydrogen bonds : bond 0.04432 ( 437) hydrogen bonds : angle 4.59400 ( 1242) link_BETA1-4 : bond 0.00229 ( 1) link_BETA1-4 : angle 2.14141 ( 3) link_NAG-ASN : bond 0.00387 ( 2) link_NAG-ASN : angle 3.05460 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.359 Fit side-chains REVERT: A 170 LEU cc_start: 0.8224 (mt) cc_final: 0.7835 (tm) REVERT: A 507 MET cc_start: 0.7484 (ptt) cc_final: 0.6823 (pp-130) REVERT: A 593 ASP cc_start: 0.8198 (t0) cc_final: 0.7940 (t70) REVERT: A 654 GLN cc_start: 0.8151 (mt0) cc_final: 0.7739 (mt0) REVERT: A 679 ASP cc_start: 0.8496 (m-30) cc_final: 0.8200 (m-30) REVERT: A 847 GLU cc_start: 0.8098 (pm20) cc_final: 0.7779 (pm20) REVERT: B 17 TRP cc_start: 0.6508 (t-100) cc_final: 0.5931 (t60) outliers start: 22 outliers final: 5 residues processed: 134 average time/residue: 0.6167 time to fit residues: 88.6831 Evaluate side-chains 102 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 15 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112624 restraints weight = 16625.519| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.11 r_work: 0.3251 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10933 Z= 0.170 Angle : 1.494 31.772 14845 Z= 0.557 Chirality : 0.145 1.865 1681 Planarity : 0.005 0.050 1869 Dihedral : 29.385 179.731 1961 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.38 % Allowed : 13.92 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1315 helix: 0.01 (0.22), residues: 567 sheet: -0.46 (0.39), residues: 155 loop : -1.64 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.030 0.002 TYR B 243 PHE 0.020 0.002 PHE A 922 TRP 0.015 0.002 TRP A 392 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00412 (10925) covalent geometry : angle 1.49210 (14826) SS BOND : bond 0.01030 ( 5) SS BOND : angle 2.07697 ( 10) hydrogen bonds : bond 0.04812 ( 437) hydrogen bonds : angle 4.42214 ( 1242) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 2.21612 ( 3) link_NAG-ASN : bond 0.00352 ( 2) link_NAG-ASN : angle 3.14882 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.409 Fit side-chains REVERT: A 170 LEU cc_start: 0.8168 (mt) cc_final: 0.7752 (tm) REVERT: A 192 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: A 593 ASP cc_start: 0.8172 (t0) cc_final: 0.7903 (t70) REVERT: A 654 GLN cc_start: 0.8082 (mt0) cc_final: 0.7666 (mt0) REVERT: A 679 ASP cc_start: 0.8521 (m-30) cc_final: 0.8203 (m-30) REVERT: A 847 GLU cc_start: 0.8170 (pm20) cc_final: 0.7897 (pm20) REVERT: B 17 TRP cc_start: 0.6584 (t-100) cc_final: 0.6010 (t60) outliers start: 27 outliers final: 10 residues processed: 123 average time/residue: 0.5695 time to fit residues: 75.7252 Evaluate side-chains 100 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 540 ASN ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108988 restraints weight = 16758.921| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.80 r_work: 0.3296 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10933 Z= 0.119 Angle : 1.461 32.297 14845 Z= 0.535 Chirality : 0.144 1.860 1681 Planarity : 0.005 0.047 1869 Dihedral : 29.138 178.959 1961 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.11 % Allowed : 15.59 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.65 (0.23), residues: 1315 helix: 0.54 (0.23), residues: 560 sheet: -0.25 (0.40), residues: 155 loop : -1.40 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 893 TYR 0.021 0.001 TYR B 243 PHE 0.012 0.001 PHE B 295 TRP 0.017 0.001 TRP A 418 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00277 (10925) covalent geometry : angle 1.46057 (14826) SS BOND : bond 0.00719 ( 5) SS BOND : angle 1.49687 ( 10) hydrogen bonds : bond 0.03793 ( 437) hydrogen bonds : angle 4.16563 ( 1242) link_BETA1-4 : bond 0.00060 ( 1) link_BETA1-4 : angle 1.86153 ( 3) link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 2.77530 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8152 (mt) cc_final: 0.7746 (tm) REVERT: A 192 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 289 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7383 (pp20) REVERT: A 419 LEU cc_start: 0.7656 (mp) cc_final: 0.7406 (pp) REVERT: A 423 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6994 (ptp90) REVERT: A 453 GLU cc_start: 0.7885 (mp0) cc_final: 0.7472 (pt0) REVERT: A 593 ASP cc_start: 0.8130 (t0) cc_final: 0.7892 (t70) REVERT: A 654 GLN cc_start: 0.8042 (mt0) cc_final: 0.7668 (mt0) REVERT: A 679 ASP cc_start: 0.8426 (m-30) cc_final: 0.8069 (m-30) REVERT: A 852 MET cc_start: 0.8697 (mmm) cc_final: 0.8491 (mmm) REVERT: B 17 TRP cc_start: 0.6563 (t-100) cc_final: 0.6023 (t60) REVERT: B 80 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7215 (tp) REVERT: B 126 CYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5380 (p) REVERT: B 177 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8909 (mp) outliers start: 24 outliers final: 7 residues processed: 132 average time/residue: 0.5918 time to fit residues: 83.9450 Evaluate side-chains 106 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107243 restraints weight = 16632.365| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.77 r_work: 0.3263 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10933 Z= 0.155 Angle : 1.478 32.002 14845 Z= 0.547 Chirality : 0.144 1.863 1681 Planarity : 0.005 0.048 1869 Dihedral : 29.140 179.864 1961 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.82 % Allowed : 16.21 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.54 (0.23), residues: 1315 helix: 0.58 (0.23), residues: 570 sheet: -0.20 (0.40), residues: 155 loop : -1.31 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.026 0.002 TYR B 243 PHE 0.017 0.002 PHE A 922 TRP 0.015 0.001 TRP A 418 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00377 (10925) covalent geometry : angle 1.47656 (14826) SS BOND : bond 0.00837 ( 5) SS BOND : angle 1.81126 ( 10) hydrogen bonds : bond 0.04400 ( 437) hydrogen bonds : angle 4.23188 ( 1242) link_BETA1-4 : bond 0.00091 ( 1) link_BETA1-4 : angle 1.99276 ( 3) link_NAG-ASN : bond 0.00287 ( 2) link_NAG-ASN : angle 2.94308 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8145 (mt) cc_final: 0.7750 (tm) REVERT: A 192 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: A 289 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7437 (pp20) REVERT: A 391 MET cc_start: 0.8107 (mtm) cc_final: 0.7876 (mtt) REVERT: A 423 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6779 (ptp90) REVERT: A 479 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5739 (pp20) REVERT: A 593 ASP cc_start: 0.8107 (t0) cc_final: 0.7862 (t70) REVERT: A 654 GLN cc_start: 0.8056 (mt0) cc_final: 0.7678 (mt0) REVERT: A 679 ASP cc_start: 0.8408 (m-30) cc_final: 0.8072 (m-30) REVERT: A 847 GLU cc_start: 0.8269 (pm20) cc_final: 0.8060 (pm20) REVERT: A 954 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8863 (tp) REVERT: B 17 TRP cc_start: 0.6577 (t-100) cc_final: 0.6052 (t60) REVERT: B 80 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7223 (tp) REVERT: B 126 CYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5481 (p) REVERT: B 177 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9008 (mp) outliers start: 32 outliers final: 13 residues processed: 121 average time/residue: 0.5988 time to fit residues: 77.7950 Evaluate side-chains 110 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 107 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106490 restraints weight = 16696.028| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.78 r_work: 0.3257 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10933 Z= 0.170 Angle : 1.488 32.021 14845 Z= 0.553 Chirality : 0.144 1.858 1681 Planarity : 0.005 0.048 1869 Dihedral : 29.134 179.920 1961 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.91 % Allowed : 16.56 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.48 (0.23), residues: 1315 helix: 0.61 (0.23), residues: 570 sheet: -0.11 (0.40), residues: 155 loop : -1.28 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 430 TYR 0.029 0.002 TYR B 243 PHE 0.018 0.002 PHE A 922 TRP 0.015 0.002 TRP A 418 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00416 (10925) covalent geometry : angle 1.48670 (14826) SS BOND : bond 0.00815 ( 5) SS BOND : angle 1.78344 ( 10) hydrogen bonds : bond 0.04578 ( 437) hydrogen bonds : angle 4.25255 ( 1242) link_BETA1-4 : bond 0.00120 ( 1) link_BETA1-4 : angle 2.00561 ( 3) link_NAG-ASN : bond 0.00286 ( 2) link_NAG-ASN : angle 3.03188 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8149 (mt) cc_final: 0.7756 (tm) REVERT: A 192 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: A 198 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6820 (ttm170) REVERT: A 289 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7467 (pp20) REVERT: A 391 MET cc_start: 0.8115 (mtm) cc_final: 0.7863 (mtt) REVERT: A 423 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6800 (ptp90) REVERT: A 593 ASP cc_start: 0.8113 (t0) cc_final: 0.7871 (t70) REVERT: A 654 GLN cc_start: 0.8111 (mt0) cc_final: 0.7897 (mt0) REVERT: A 679 ASP cc_start: 0.8420 (m-30) cc_final: 0.8109 (m-30) REVERT: A 847 GLU cc_start: 0.8280 (pm20) cc_final: 0.8063 (pm20) REVERT: A 954 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8818 (tp) REVERT: B 17 TRP cc_start: 0.6558 (t-100) cc_final: 0.5982 (t60) REVERT: B 80 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7305 (tp) REVERT: B 126 CYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5476 (p) REVERT: B 177 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9043 (mp) outliers start: 33 outliers final: 13 residues processed: 117 average time/residue: 0.5820 time to fit residues: 73.5212 Evaluate side-chains 111 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.0370 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108787 restraints weight = 16515.976| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.78 r_work: 0.3295 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10933 Z= 0.117 Angle : 1.464 32.259 14845 Z= 0.537 Chirality : 0.144 1.862 1681 Planarity : 0.004 0.047 1869 Dihedral : 28.955 178.938 1961 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.38 % Allowed : 17.18 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.19 (0.23), residues: 1315 helix: 0.87 (0.23), residues: 572 sheet: -0.06 (0.39), residues: 157 loop : -1.13 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.020 0.001 TYR B 243 PHE 0.018 0.001 PHE B 139 TRP 0.015 0.001 TRP A 418 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00272 (10925) covalent geometry : angle 1.46331 (14826) SS BOND : bond 0.00576 ( 5) SS BOND : angle 1.43547 ( 10) hydrogen bonds : bond 0.03700 ( 437) hydrogen bonds : angle 4.10851 ( 1242) link_BETA1-4 : bond 0.00115 ( 1) link_BETA1-4 : angle 1.79457 ( 3) link_NAG-ASN : bond 0.00217 ( 2) link_NAG-ASN : angle 2.75186 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8141 (mt) cc_final: 0.7750 (tm) REVERT: A 190 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7870 (tm) REVERT: A 192 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: A 198 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6781 (ttm170) REVERT: A 289 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7385 (pp20) REVERT: A 391 MET cc_start: 0.8138 (mtm) cc_final: 0.7894 (mtt) REVERT: A 423 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6875 (ptp90) REVERT: A 427 LEU cc_start: 0.7705 (mt) cc_final: 0.7441 (mm) REVERT: A 593 ASP cc_start: 0.8066 (t0) cc_final: 0.7811 (t70) REVERT: A 654 GLN cc_start: 0.8074 (mt0) cc_final: 0.7688 (mt0) REVERT: A 679 ASP cc_start: 0.8466 (m-30) cc_final: 0.8118 (m-30) REVERT: A 847 GLU cc_start: 0.8286 (pm20) cc_final: 0.8069 (pm20) REVERT: B 17 TRP cc_start: 0.6562 (t-100) cc_final: 0.5968 (t60) REVERT: B 126 CYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5458 (p) outliers start: 27 outliers final: 12 residues processed: 127 average time/residue: 0.6131 time to fit residues: 83.8611 Evaluate side-chains 109 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 121 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110176 restraints weight = 16500.828| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.81 r_work: 0.3317 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10933 Z= 0.112 Angle : 1.457 32.207 14845 Z= 0.534 Chirality : 0.145 1.870 1681 Planarity : 0.004 0.049 1869 Dihedral : 28.829 179.104 1961 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.85 % Allowed : 18.41 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.13 (0.24), residues: 1315 helix: 1.20 (0.23), residues: 561 sheet: -0.01 (0.41), residues: 155 loop : -0.95 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.014 0.001 TYR B 243 PHE 0.025 0.001 PHE A 585 TRP 0.013 0.001 TRP A 418 HIS 0.007 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00260 (10925) covalent geometry : angle 1.45602 (14826) SS BOND : bond 0.00648 ( 5) SS BOND : angle 2.25904 ( 10) hydrogen bonds : bond 0.03312 ( 437) hydrogen bonds : angle 4.11316 ( 1242) link_BETA1-4 : bond 0.00052 ( 1) link_BETA1-4 : angle 1.69952 ( 3) link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 2.56147 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8626 (mp) cc_final: 0.8361 (mt) REVERT: A 170 LEU cc_start: 0.8099 (mt) cc_final: 0.7694 (tm) REVERT: A 198 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6749 (ttm170) REVERT: A 289 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7351 (pp20) REVERT: A 391 MET cc_start: 0.8073 (mtm) cc_final: 0.7855 (mtt) REVERT: A 418 TRP cc_start: 0.7484 (t-100) cc_final: 0.7090 (t-100) REVERT: A 427 LEU cc_start: 0.7638 (mt) cc_final: 0.7413 (mm) REVERT: A 507 MET cc_start: 0.6976 (ptp) cc_final: 0.6645 (ppp) REVERT: A 593 ASP cc_start: 0.8044 (t0) cc_final: 0.7815 (t70) REVERT: A 654 GLN cc_start: 0.8055 (mt0) cc_final: 0.7667 (mt0) REVERT: A 679 ASP cc_start: 0.8479 (m-30) cc_final: 0.8153 (m-30) REVERT: A 847 GLU cc_start: 0.8314 (pm20) cc_final: 0.8091 (pm20) REVERT: B 17 TRP cc_start: 0.6593 (t-100) cc_final: 0.6120 (t60) REVERT: B 126 CYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5536 (p) outliers start: 21 outliers final: 9 residues processed: 120 average time/residue: 0.5943 time to fit residues: 77.0544 Evaluate side-chains 106 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109524 restraints weight = 16534.594| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.79 r_work: 0.3303 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10933 Z= 0.118 Angle : 1.459 32.032 14845 Z= 0.535 Chirality : 0.145 1.871 1681 Planarity : 0.004 0.051 1869 Dihedral : 28.787 179.359 1961 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.15 % Allowed : 19.12 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.20 (0.24), residues: 1315 helix: 1.18 (0.23), residues: 567 sheet: 0.07 (0.41), residues: 155 loop : -0.85 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.018 0.001 TYR B 243 PHE 0.011 0.001 PHE B 42 TRP 0.014 0.001 TRP A 392 HIS 0.002 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00286 (10925) covalent geometry : angle 1.45749 (14826) SS BOND : bond 0.00505 ( 5) SS BOND : angle 2.58807 ( 10) hydrogen bonds : bond 0.03528 ( 437) hydrogen bonds : angle 4.12451 ( 1242) link_BETA1-4 : bond 0.00152 ( 1) link_BETA1-4 : angle 1.71278 ( 3) link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 2.54077 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8576 (mp) cc_final: 0.8309 (mt) REVERT: A 170 LEU cc_start: 0.8047 (mt) cc_final: 0.7696 (tm) REVERT: A 198 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6725 (ttm170) REVERT: A 289 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7367 (pp20) REVERT: A 391 MET cc_start: 0.8087 (mtm) cc_final: 0.7867 (mtt) REVERT: A 418 TRP cc_start: 0.7471 (t-100) cc_final: 0.7126 (t-100) REVERT: A 593 ASP cc_start: 0.8065 (t0) cc_final: 0.7837 (t70) REVERT: A 654 GLN cc_start: 0.8100 (mt0) cc_final: 0.7736 (mt0) REVERT: A 679 ASP cc_start: 0.8476 (m-30) cc_final: 0.8159 (m-30) REVERT: B 17 TRP cc_start: 0.6634 (t-100) cc_final: 0.6118 (t60) REVERT: B 126 CYS cc_start: 0.6026 (OUTLIER) cc_final: 0.5539 (p) outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.5841 time to fit residues: 72.4450 Evaluate side-chains 102 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 556 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 63 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107742 restraints weight = 16554.494| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.78 r_work: 0.3270 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10933 Z= 0.145 Angle : 1.478 31.961 14845 Z= 0.547 Chirality : 0.145 1.892 1681 Planarity : 0.005 0.050 1869 Dihedral : 28.829 178.934 1961 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.41 % Allowed : 19.21 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.24), residues: 1315 helix: 1.04 (0.23), residues: 571 sheet: 0.05 (0.41), residues: 155 loop : -0.92 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.023 0.001 TYR B 243 PHE 0.015 0.001 PHE A 922 TRP 0.012 0.001 TRP A 418 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00357 (10925) covalent geometry : angle 1.47616 (14826) SS BOND : bond 0.00734 ( 5) SS BOND : angle 2.65456 ( 10) hydrogen bonds : bond 0.04130 ( 437) hydrogen bonds : angle 4.19199 ( 1242) link_BETA1-4 : bond 0.00063 ( 1) link_BETA1-4 : angle 1.80670 ( 3) link_NAG-ASN : bond 0.00265 ( 2) link_NAG-ASN : angle 2.71101 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8609 (mp) cc_final: 0.8329 (mt) REVERT: A 170 LEU cc_start: 0.8018 (mt) cc_final: 0.7662 (tm) REVERT: A 198 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6799 (ttm170) REVERT: A 251 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6647 (pt0) REVERT: A 289 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7402 (pp20) REVERT: A 391 MET cc_start: 0.8143 (mtm) cc_final: 0.7909 (mtt) REVERT: A 418 TRP cc_start: 0.7332 (t-100) cc_final: 0.6904 (t-100) REVERT: A 593 ASP cc_start: 0.8098 (t0) cc_final: 0.7865 (t70) REVERT: A 679 ASP cc_start: 0.8442 (m-30) cc_final: 0.8155 (m-30) REVERT: A 847 GLU cc_start: 0.8272 (pm20) cc_final: 0.8052 (pm20) REVERT: B 17 TRP cc_start: 0.6549 (t-100) cc_final: 0.6033 (t60) REVERT: B 126 CYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5487 (p) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.5655 time to fit residues: 65.3713 Evaluate side-chains 104 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 556 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 81 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.0010 chunk 83 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111270 restraints weight = 16625.273| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.80 r_work: 0.3324 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10933 Z= 0.109 Angle : 1.451 32.049 14845 Z= 0.530 Chirality : 0.144 1.862 1681 Planarity : 0.004 0.049 1869 Dihedral : 28.721 177.466 1961 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.41 % Allowed : 19.21 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1315 helix: 1.38 (0.23), residues: 561 sheet: 0.17 (0.42), residues: 153 loop : -0.80 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.016 0.001 TYR A 488 PHE 0.010 0.001 PHE B 295 TRP 0.013 0.001 TRP A 392 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00254 (10925) covalent geometry : angle 1.45011 (14826) SS BOND : bond 0.00527 ( 5) SS BOND : angle 2.30862 ( 10) hydrogen bonds : bond 0.03052 ( 437) hydrogen bonds : angle 4.03240 ( 1242) link_BETA1-4 : bond 0.00070 ( 1) link_BETA1-4 : angle 1.51156 ( 3) link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 2.40432 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.20 seconds wall clock time: 76 minutes 39.26 seconds (4599.26 seconds total)