Starting phenix.real_space_refine on Fri Jul 3 00:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e20_30948/07_2026/7e20_30948_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e20_30948/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e20_30948/07_2026/7e20_30948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e20_30948/07_2026/7e20_30948.map" model { file = "/net/cci-nas-00/data/ceres_data/7e20_30948/07_2026/7e20_30948_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e20_30948/07_2026/7e20_30948_neut.cif" } 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-6108/lib/python3.11/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, 160 Ad-hoc single atom residues: {' K': 3} Unusual residues: {' MG': 1, 'PC1': 1, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 3 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: 2.04, per 1000 atoms: 0.19 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: 0.63 Conformation dependent library (CDL) restraints added in 343.2 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: 0.36 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: 1.84 Time building geometry restraints manager: 0.86 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.520 Find NCS groups from input model: 0.050 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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/Z covalent geometry : bond 0.01229 / 0.58 (10925) covalent geometry : angle 1.32834 / 0.62 (14826) SS BOND : bond 0.06866 / 3.43 ( 5) SS BOND : angle 13.00392 / 10.41 ( 10) hydrogen bonds : bond 0.17697 / 12.08 ( 437) hydrogen bonds : angle 6.58020 / 4.53 ( 1242) link_BETA1-4 : bond 0.00045 / 0.02 ( 1) link_BETA1-4 : angle 3.37254 / 1.76 ( 3) link_NAG-ASN : bond 0.00463 / 0.23 ( 2) link_NAG-ASN : angle 4.01343 / 2.22 ( 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 : 0.392 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: 0.4867 (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: 0.7206 (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: 0.7283 time to fit residues: 128.6530 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 : 0.411 ------------------------------------------------------------------------------- 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... 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 = 0.3883 r_free = 0.3883 target = 0.145679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113534 restraints weight = 16501.851| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.06 r_work: 0.3277 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10933 Z= 0.132 Angle : 1.492 33.881 14845 Z= 0.553 Chirality : 0.145 1.842 1681 Planarity : 0.006 0.058 1869 Dihedral : 29.455 179.407 1964 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.76 % Allowed : 12.33 % Favored : 85.90 % 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: -1.82 (0.22), residues: 1315 helix: -0.65 (0.21), residues: 559 sheet: -0.59 (0.38), residues: 161 loop : -1.88 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.027 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/Z covalent geometry : bond 0.00292 / 0.13 (10925) covalent geometry : angle 1.48952 / 0.55 (14826) SS BOND : bond 0.00531 / 0.26 ( 5) SS BOND : angle 2.48865 / 1.70 ( 10) hydrogen bonds : bond 0.04387 / 2.97 ( 437) hydrogen bonds : angle 4.57162 / 3.15 ( 1242) link_BETA1-4 : bond 0.00150 / 0.08 ( 1) link_BETA1-4 : angle 2.14814 / 1.11 ( 3) link_NAG-ASN : bond 0.00356 / 0.19 ( 2) link_NAG-ASN : angle 3.01655 / 1.61 ( 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 142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.431 Fit side-chains REVERT: A 170 LEU cc_start: 0.8221 (mt) cc_final: 0.7843 (tm) REVERT: A 593 ASP cc_start: 0.8198 (t0) cc_final: 0.7949 (t70) REVERT: A 654 GLN cc_start: 0.8143 (mt0) cc_final: 0.7730 (mt0) REVERT: A 679 ASP cc_start: 0.8506 (m-30) cc_final: 0.8192 (m-30) REVERT: A 847 GLU cc_start: 0.8108 (pm20) cc_final: 0.7824 (pm20) REVERT: B 17 TRP cc_start: 0.6504 (t-100) cc_final: 0.5932 (t60) REVERT: B 192 LYS cc_start: 0.8237 (pttm) cc_final: 0.8032 (pttm) outliers start: 20 outliers final: 4 residues processed: 135 average time/residue: 0.6236 time to fit residues: 90.7342 Evaluate side-chains 101 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 117 optimal weight: 0.0570 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 ASN A 582 ASN B 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111588 restraints weight = 16655.617| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.42 r_work: 0.3241 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10933 Z= 0.174 Angle : 1.497 31.801 14845 Z= 0.559 Chirality : 0.145 1.863 1681 Planarity : 0.005 0.050 1869 Dihedral : 29.376 179.628 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 : 2.29 % Allowed : 13.92 % Favored : 83.79 % 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: -1.21 (0.23), residues: 1315 helix: -0.02 (0.22), residues: 567 sheet: -0.45 (0.39), residues: 155 loop : -1.64 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.029 0.002 TYR B 243 PHE 0.021 0.002 PHE A 922 TRP 0.016 0.002 TRP A 418 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (10925) covalent geometry : angle 1.49574 / 0.56 (14826) SS BOND : bond 0.00945 / 0.48 ( 5) SS BOND : angle 2.11229 / 1.68 ( 10) hydrogen bonds : bond 0.04872 / 3.30 ( 437) hydrogen bonds : angle 4.42519 / 3.04 ( 1242) link_BETA1-4 : bond 0.00074 / 0.04 ( 1) link_BETA1-4 : angle 2.21764 / 1.15 ( 3) link_NAG-ASN : bond 0.00354 / 0.18 ( 2) link_NAG-ASN : angle 3.14830 / 1.71 ( 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 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.440 Fit side-chains REVERT: A 170 LEU cc_start: 0.8173 (mt) cc_final: 0.7744 (tm) REVERT: A 192 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: A 593 ASP cc_start: 0.8186 (t0) cc_final: 0.7913 (t70) REVERT: A 654 GLN cc_start: 0.8119 (mt0) cc_final: 0.7702 (mt0) REVERT: A 679 ASP cc_start: 0.8551 (m-30) cc_final: 0.8232 (m-30) REVERT: A 847 GLU cc_start: 0.8198 (pm20) cc_final: 0.7929 (pm20) REVERT: B 17 TRP cc_start: 0.6605 (t-100) cc_final: 0.6009 (t60) outliers start: 26 outliers final: 10 residues processed: 125 average time/residue: 0.5848 time to fit residues: 79.3077 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 : 0.429 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 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: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 540 ASN A 876 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107992 restraints weight = 16726.811| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.80 r_work: 0.3284 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10933 Z= 0.135 Angle : 1.472 32.180 14845 Z= 0.542 Chirality : 0.144 1.856 1681 Planarity : 0.005 0.048 1869 Dihedral : 29.174 179.873 1961 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.47 % Allowed : 15.42 % Favored : 82.11 % 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: -0.75 (0.23), residues: 1315 helix: 0.44 (0.22), residues: 567 sheet: -0.25 (0.40), residues: 155 loop : -1.48 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 893 TYR 0.024 0.001 TYR B 243 PHE 0.013 0.001 PHE A 922 TRP 0.015 0.001 TRP A 392 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (10925) covalent geometry : angle 1.47070 / 0.54 (14826) SS BOND : bond 0.00883 / 0.45 ( 5) SS BOND : angle 1.54447 / 1.31 ( 10) hydrogen bonds : bond 0.04124 / 2.79 ( 437) hydrogen bonds : angle 4.21293 / 2.88 ( 1242) link_BETA1-4 : bond 0.00110 / 0.06 ( 1) link_BETA1-4 : angle 1.91659 / 0.99 ( 3) link_NAG-ASN : bond 0.00242 / 0.13 ( 2) link_NAG-ASN : angle 2.89080 / 1.56 ( 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 138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5131 (mtm-85) REVERT: A 170 LEU cc_start: 0.8165 (mt) cc_final: 0.7753 (tm) REVERT: A 192 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: A 289 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7432 (pp20) REVERT: A 453 GLU cc_start: 0.7896 (mp0) cc_final: 0.7494 (pt0) REVERT: A 593 ASP cc_start: 0.8148 (t0) cc_final: 0.7939 (t70) REVERT: A 654 GLN cc_start: 0.8068 (mt0) cc_final: 0.7692 (mt0) REVERT: A 679 ASP cc_start: 0.8410 (m-30) cc_final: 0.8089 (m-30) REVERT: B 17 TRP cc_start: 0.6570 (t-100) cc_final: 0.6035 (t60) REVERT: B 80 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7287 (tp) REVERT: B 126 CYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5560 (p) REVERT: B 177 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8994 (mp) outliers start: 28 outliers final: 9 residues processed: 130 average time/residue: 0.6057 time to fit residues: 85.2185 Evaluate side-chains 109 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 506 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 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: 0.9990 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112668 restraints weight = 16641.118| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.18 r_work: 0.3269 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10933 Z= 0.154 Angle : 1.479 32.052 14845 Z= 0.548 Chirality : 0.144 1.862 1681 Planarity : 0.005 0.049 1869 Dihedral : 29.147 179.917 1961 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.08 % Allowed : 15.86 % Favored : 81.06 % 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: -0.55 (0.23), residues: 1315 helix: 0.57 (0.23), residues: 568 sheet: -0.13 (0.39), residues: 157 loop : -1.34 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.026 0.001 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/Z covalent geometry : bond 0.00370 / 0.15 (10925) covalent geometry : angle 1.47827 / 0.55 (14826) SS BOND : bond 0.00823 / 0.42 ( 5) SS BOND : angle 1.67187 / 1.41 ( 10) hydrogen bonds : bond 0.04394 / 2.97 ( 437) hydrogen bonds : angle 4.23486 / 2.91 ( 1242) link_BETA1-4 : bond 0.00086 / 0.05 ( 1) link_BETA1-4 : angle 2.01161 / 1.04 ( 3) link_NAG-ASN : bond 0.00300 / 0.16 ( 2) link_NAG-ASN : angle 2.95757 / 1.61 ( 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 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5080 (mtm-85) REVERT: A 170 LEU cc_start: 0.8158 (mt) cc_final: 0.7738 (tm) REVERT: A 192 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: A 289 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7455 (pp20) REVERT: A 391 MET cc_start: 0.8076 (mtm) cc_final: 0.7850 (mtt) REVERT: A 423 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6796 (ptp90) REVERT: A 591 MET cc_start: 0.8591 (mtm) cc_final: 0.8225 (mtp) REVERT: A 593 ASP cc_start: 0.8118 (t0) cc_final: 0.7873 (t70) REVERT: A 654 GLN cc_start: 0.8112 (mt0) cc_final: 0.7730 (mt0) REVERT: A 679 ASP cc_start: 0.8424 (m-30) cc_final: 0.8076 (m-30) REVERT: A 847 GLU cc_start: 0.8275 (pm20) cc_final: 0.8035 (pm20) REVERT: A 954 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8858 (tp) REVERT: B 17 TRP cc_start: 0.6552 (t-100) cc_final: 0.5951 (t60) REVERT: B 80 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7346 (tp) REVERT: B 126 CYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5559 (p) REVERT: B 177 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9034 (mp) outliers start: 35 outliers final: 13 residues processed: 128 average time/residue: 0.6066 time to fit residues: 83.8003 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 : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A 540 ASN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105560 restraints weight = 16744.230| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.77 r_work: 0.3245 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10933 Z= 0.197 Angle : 1.502 31.976 14845 Z= 0.563 Chirality : 0.145 1.871 1681 Planarity : 0.005 0.050 1869 Dihedral : 29.191 179.865 1961 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.26 % Allowed : 16.74 % Favored : 80.00 % 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: -0.59 (0.23), residues: 1315 helix: 0.50 (0.22), residues: 570 sheet: -0.12 (0.40), residues: 155 loop : -1.33 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 430 TYR 0.033 0.002 TYR B 243 PHE 0.020 0.002 PHE A 922 TRP 0.013 0.002 TRP A 418 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (10925) covalent geometry : angle 1.50043 / 0.56 (14826) SS BOND : bond 0.00960 / 0.49 ( 5) SS BOND : angle 2.01622 / 1.70 ( 10) hydrogen bonds : bond 0.04967 / 3.35 ( 437) hydrogen bonds : angle 4.36492 / 3.00 ( 1242) link_BETA1-4 : bond 0.00183 / 0.10 ( 1) link_BETA1-4 : angle 2.12086 / 1.10 ( 3) link_NAG-ASN : bond 0.00322 / 0.16 ( 2) link_NAG-ASN : angle 3.17581 / 1.74 ( 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 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5051 (mtm-85) REVERT: A 170 LEU cc_start: 0.8172 (mt) cc_final: 0.7763 (tm) REVERT: A 192 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: A 391 MET cc_start: 0.8121 (mtm) cc_final: 0.7873 (mtt) REVERT: A 423 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6778 (ptp90) REVERT: A 593 ASP cc_start: 0.8111 (t0) cc_final: 0.7867 (t70) REVERT: A 654 GLN cc_start: 0.8133 (mt0) cc_final: 0.7916 (mt0) REVERT: A 679 ASP cc_start: 0.8412 (m-30) cc_final: 0.8139 (m-30) REVERT: A 954 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 17 TRP cc_start: 0.6544 (t-100) cc_final: 0.6009 (t60) REVERT: B 80 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7302 (tp) REVERT: B 126 CYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5530 (p) REVERT: B 177 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9067 (mp) outliers start: 37 outliers final: 15 residues processed: 121 average time/residue: 0.5692 time to fit residues: 74.8245 Evaluate side-chains 110 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 304 VAL Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 530 LEU 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: 2.9990 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107519 restraints weight = 16538.767| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.76 r_work: 0.3280 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10933 Z= 0.136 Angle : 1.474 32.153 14845 Z= 0.544 Chirality : 0.145 1.856 1681 Planarity : 0.005 0.048 1869 Dihedral : 29.023 179.845 1961 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.56 % Allowed : 17.09 % Favored : 80.35 % 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: -0.34 (0.23), residues: 1315 helix: 0.77 (0.23), residues: 568 sheet: -0.11 (0.40), residues: 155 loop : -1.22 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.024 0.001 TYR B 243 PHE 0.018 0.001 PHE B 139 TRP 0.014 0.001 TRP A 418 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10925) covalent geometry : angle 1.47291 / 0.54 (14826) SS BOND : bond 0.00699 / 0.35 ( 5) SS BOND : angle 1.61950 / 1.39 ( 10) hydrogen bonds : bond 0.04095 / 2.77 ( 437) hydrogen bonds : angle 4.22853 / 2.90 ( 1242) link_BETA1-4 : bond 0.00091 / 0.05 ( 1) link_BETA1-4 : angle 1.89348 / 0.98 ( 3) link_NAG-ASN : bond 0.00215 / 0.11 ( 2) link_NAG-ASN : angle 2.89440 / 1.57 ( 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 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.5069 (mtm-85) REVERT: A 117 ILE cc_start: 0.8632 (mp) cc_final: 0.8291 (mt) REVERT: A 170 LEU cc_start: 0.8148 (mt) cc_final: 0.7747 (tm) REVERT: A 192 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 289 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7440 (pp20) REVERT: A 391 MET cc_start: 0.8103 (mtm) cc_final: 0.7845 (mtt) REVERT: A 423 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6857 (ptp90) REVERT: A 427 LEU cc_start: 0.7671 (mt) cc_final: 0.7378 (mm) REVERT: A 507 MET cc_start: 0.7117 (ptp) cc_final: 0.6682 (ttp) REVERT: A 539 GLN cc_start: 0.8333 (mm110) cc_final: 0.8122 (mm-40) REVERT: A 593 ASP cc_start: 0.8090 (t0) cc_final: 0.7844 (t70) REVERT: A 679 ASP cc_start: 0.8440 (m-30) cc_final: 0.8128 (m-30) REVERT: A 847 GLU cc_start: 0.8267 (pm20) cc_final: 0.8056 (pm20) REVERT: A 954 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8754 (tp) REVERT: B 17 TRP cc_start: 0.6558 (t-100) cc_final: 0.6016 (t60) REVERT: B 126 CYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5496 (p) REVERT: B 177 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8934 (mp) outliers start: 29 outliers final: 14 residues processed: 126 average time/residue: 0.5901 time to fit residues: 80.5085 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 : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 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 589 ILE 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 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 162 LEU Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 111 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 HIS A 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106186 restraints weight = 16537.684| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.78 r_work: 0.3261 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10933 Z= 0.172 Angle : 1.492 32.017 14845 Z= 0.555 Chirality : 0.145 1.895 1681 Planarity : 0.005 0.049 1869 Dihedral : 29.002 179.662 1961 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.64 % Allowed : 17.80 % Favored : 79.56 % 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: -0.36 (0.23), residues: 1315 helix: 0.69 (0.23), residues: 571 sheet: -0.06 (0.40), residues: 155 loop : -1.18 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.029 0.002 TYR B 243 PHE 0.017 0.002 PHE A 922 TRP 0.013 0.001 TRP A 418 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (10925) covalent geometry : angle 1.49110 / 0.55 (14826) SS BOND : bond 0.00800 / 0.40 ( 5) SS BOND : angle 1.78393 / 1.53 ( 10) hydrogen bonds : bond 0.04613 / 3.12 ( 437) hydrogen bonds : angle 4.29544 / 2.96 ( 1242) link_BETA1-4 : bond 0.00123 / 0.06 ( 1) link_BETA1-4 : angle 2.04445 / 1.06 ( 3) link_NAG-ASN : bond 0.00323 / 0.17 ( 2) link_NAG-ASN : angle 3.06160 / 1.68 ( 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 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5125 (mtm-85) REVERT: A 117 ILE cc_start: 0.8602 (mp) cc_final: 0.8282 (mt) REVERT: A 170 LEU cc_start: 0.8148 (mt) cc_final: 0.7706 (tm) REVERT: A 192 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: A 289 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7475 (pp20) REVERT: A 391 MET cc_start: 0.8120 (mtm) cc_final: 0.7843 (mtt) REVERT: A 423 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6977 (ptp90) REVERT: A 427 LEU cc_start: 0.7803 (mt) cc_final: 0.7543 (mm) REVERT: A 507 MET cc_start: 0.7088 (ptp) cc_final: 0.6635 (ttp) REVERT: A 539 GLN cc_start: 0.8388 (mm110) cc_final: 0.8138 (mm-40) REVERT: A 593 ASP cc_start: 0.8107 (t0) cc_final: 0.7870 (t70) REVERT: A 679 ASP cc_start: 0.8418 (m-30) cc_final: 0.8104 (m-30) REVERT: A 954 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8854 (tp) REVERT: B 17 TRP cc_start: 0.6563 (t-100) cc_final: 0.6010 (t60) REVERT: B 126 CYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5491 (p) outliers start: 30 outliers final: 14 residues processed: 113 average time/residue: 0.5762 time to fit residues: 70.4728 Evaluate side-chains 107 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 32 MET 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 192 GLU Chi-restraints excluded: chain A residue 423 ARG 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3889 r_free = 0.3889 target = 0.146329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109220 restraints weight = 16533.351| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.78 r_work: 0.3298 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10933 Z= 0.115 Angle : 1.460 32.242 14845 Z= 0.534 Chirality : 0.145 1.859 1681 Planarity : 0.004 0.047 1869 Dihedral : 28.825 178.572 1961 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.76 % Allowed : 18.59 % Favored : 79.65 % 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: -0.05 (0.24), residues: 1315 helix: 0.98 (0.23), residues: 572 sheet: -0.04 (0.40), residues: 155 loop : -1.03 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.016 0.001 TYR B 243 PHE 0.014 0.001 PHE B 139 TRP 0.012 0.001 TRP A 418 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (10925) covalent geometry : angle 1.45908 / 0.53 (14826) SS BOND : bond 0.00611 / 0.31 ( 5) SS BOND : angle 1.38506 / 1.19 ( 10) hydrogen bonds : bond 0.03504 / 2.38 ( 437) hydrogen bonds : angle 4.10782 / 2.81 ( 1242) link_BETA1-4 : bond 0.00152 / 0.08 ( 1) link_BETA1-4 : angle 1.67506 / 0.87 ( 3) link_NAG-ASN : bond 0.00188 / 0.10 ( 2) link_NAG-ASN : angle 2.71692 / 1.47 ( 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 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5133 (mtm-85) REVERT: A 117 ILE cc_start: 0.8528 (mp) cc_final: 0.8273 (mt) REVERT: A 159 GLU cc_start: 0.7944 (mp0) cc_final: 0.7729 (mp0) REVERT: A 170 LEU cc_start: 0.8127 (mt) cc_final: 0.7679 (tm) REVERT: A 183 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 289 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7351 (pp20) REVERT: A 418 TRP cc_start: 0.7668 (t-100) cc_final: 0.7259 (t-100) REVERT: A 427 LEU cc_start: 0.7706 (mt) cc_final: 0.7416 (mm) REVERT: A 453 GLU cc_start: 0.7950 (mp0) cc_final: 0.7290 (pt0) REVERT: A 507 MET cc_start: 0.6947 (ptp) cc_final: 0.6517 (ttp) REVERT: A 593 ASP cc_start: 0.8078 (t0) cc_final: 0.7857 (t70) REVERT: A 679 ASP cc_start: 0.8471 (m-30) cc_final: 0.8127 (m-30) REVERT: A 847 GLU cc_start: 0.8309 (pm20) cc_final: 0.8073 (pm20) REVERT: B 17 TRP cc_start: 0.6548 (t-100) cc_final: 0.5990 (t60) REVERT: B 126 CYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5587 (p) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 0.5249 time to fit residues: 64.0355 Evaluate side-chains 106 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 506 VAL 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 118 ARG 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: 0.7980 chunk 64 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 540 ASN A 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110401 restraints weight = 16457.030| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.79 r_work: 0.3321 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10933 Z= 0.109 Angle : 1.451 32.160 14845 Z= 0.528 Chirality : 0.145 1.874 1681 Planarity : 0.004 0.051 1869 Dihedral : 28.737 178.691 1961 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.97 % Allowed : 19.21 % Favored : 79.82 % 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: 1.25 (0.23), residues: 560 sheet: 0.08 (0.41), residues: 155 loop : -0.91 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.015 0.001 TYR B 243 PHE 0.017 0.001 PHE A 585 TRP 0.011 0.001 TRP A 418 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10925) covalent geometry : angle 1.45028 / 0.53 (14826) SS BOND : bond 0.00664 / 0.34 ( 5) SS BOND : angle 1.31924 / 1.12 ( 10) hydrogen bonds : bond 0.03266 / 2.21 ( 437) hydrogen bonds : angle 3.99337 / 2.74 ( 1242) link_BETA1-4 : bond 0.00174 / 0.09 ( 1) link_BETA1-4 : angle 1.68440 / 0.87 ( 3) link_NAG-ASN : bond 0.00293 / 0.15 ( 2) link_NAG-ASN : angle 2.56035 / 1.40 ( 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 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.469 Fit side-chains REVERT: A 30 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5123 (mtm-85) REVERT: A 117 ILE cc_start: 0.8535 (mp) cc_final: 0.8285 (mt) REVERT: A 159 GLU cc_start: 0.7954 (mp0) cc_final: 0.7723 (mp0) REVERT: A 170 LEU cc_start: 0.7982 (mt) cc_final: 0.7610 (tm) REVERT: A 183 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7756 (mm-30) REVERT: A 289 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7310 (pp20) REVERT: A 418 TRP cc_start: 0.7575 (t-100) cc_final: 0.7237 (t-100) REVERT: A 427 LEU cc_start: 0.7727 (mt) cc_final: 0.7504 (mm) REVERT: A 453 GLU cc_start: 0.7951 (mp0) cc_final: 0.7361 (pt0) REVERT: A 507 MET cc_start: 0.6874 (ptp) cc_final: 0.6429 (ttp) REVERT: A 593 ASP cc_start: 0.8052 (t0) cc_final: 0.7826 (t0) REVERT: A 679 ASP cc_start: 0.8494 (m-30) cc_final: 0.8152 (m-30) REVERT: B 17 TRP cc_start: 0.6619 (t-100) cc_final: 0.6119 (t60) REVERT: B 126 CYS cc_start: 0.5760 (OUTLIER) cc_final: 0.5444 (p) outliers start: 11 outliers final: 6 residues processed: 115 average time/residue: 0.6195 time to fit residues: 77.1743 Evaluate side-chains 107 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 165 VAL 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 840 LYS 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: 0.0670 chunk 51 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.0010 chunk 83 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 85 optimal weight: 0.0170 chunk 27 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.3764 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.149155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112015 restraints weight = 16590.464| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.81 r_work: 0.3336 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10933 Z= 0.108 Angle : 1.452 32.108 14845 Z= 0.529 Chirality : 0.145 1.872 1681 Planarity : 0.004 0.048 1869 Dihedral : 28.703 177.759 1961 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.88 % Allowed : 19.30 % Favored : 79.82 % 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: 0.38 (0.24), residues: 1315 helix: 1.47 (0.23), residues: 552 sheet: 0.04 (0.41), residues: 156 loop : -0.83 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.011 0.001 TYR A 488 PHE 0.013 0.001 PHE A 585 TRP 0.009 0.001 TRP A 418 HIS 0.003 0.000 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10925) covalent geometry : angle 1.45010 / 0.53 (14826) SS BOND : bond 0.00400 / 0.21 ( 5) SS BOND : angle 2.63517 / 1.54 ( 10) hydrogen bonds : bond 0.02966 / 2.03 ( 437) hydrogen bonds : angle 4.05336 / 2.84 ( 1242) link_BETA1-4 : bond 0.00166 / 0.09 ( 1) link_BETA1-4 : angle 1.60621 / 0.83 ( 3) link_NAG-ASN : bond 0.00158 / 0.08 ( 2) link_NAG-ASN : angle 2.34478 / 1.27 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.35 seconds wall clock time: 76 minutes 0.41 seconds (4560.41 seconds total)