Starting phenix.real_space_refine on Tue Jul 29 07:57:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e20_30948/07_2025/7e20_30948_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e20_30948/07_2025/7e20_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_2025/7e20_30948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e20_30948/07_2025/7e20_30948.map" model { file = "/net/cci-nas-00/data/ceres_data/7e20_30948/07_2025/7e20_30948_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e20_30948/07_2025/7e20_30948_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.64, per 1000 atoms: 0.71 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: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.35 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: 3.77 Time building geometry restraints manager: 3.29 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: 0.550 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.460 ------------------------------------------------------------------------------- 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 : 9.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP A 392 HIS 0.005 0.002 HIS A 44 PHE 0.040 0.003 PHE A 291 TYR 0.040 0.002 TYR B 243 ARG 0.012 0.001 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 2) link_NAG-ASN : angle 4.01343 ( 6) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 3.37254 ( 3) hydrogen bonds : bond 0.17697 ( 437) hydrogen bonds : angle 6.58020 ( 1242) SS BOND : bond 0.06866 ( 5) SS BOND : angle 13.00392 ( 10) covalent geometry : bond 0.01229 (10925) covalent geometry : angle 1.32834 (14826) *********************** 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 : 1.225 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: 0.7207 (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: 1.4899 time to fit residues: 263.8148 Evaluate side-chains 104 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 110 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 390 HIS 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107542 restraints weight = 16421.303| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.75 r_work: 0.3266 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10933 Z= 0.152 Angle : 1.494 31.204 14845 Z= 0.560 Chirality : 0.150 1.906 1681 Planarity : 0.006 0.058 1869 Dihedral : 29.537 179.199 1964 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.03 % Allowed : 12.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.21), residues: 1315 helix: -0.76 (0.21), residues: 559 sheet: -0.67 (0.38), residues: 162 loop : -1.89 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 392 HIS 0.003 0.001 HIS A 620 PHE 0.022 0.002 PHE A 291 TYR 0.031 0.001 TYR B 243 ARG 0.007 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 2) link_NAG-ASN : angle 3.17279 ( 6) link_BETA1-4 : bond 0.00008 ( 1) link_BETA1-4 : angle 2.34585 ( 3) hydrogen bonds : bond 0.04959 ( 437) hydrogen bonds : angle 4.65831 ( 1242) SS BOND : bond 0.00588 ( 5) SS BOND : angle 2.77091 ( 10) covalent geometry : bond 0.00351 (10925) covalent geometry : angle 1.49161 (14826) *********************** 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 141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.395 Fit side-chains REVERT: A 170 LEU cc_start: 0.8178 (mt) cc_final: 0.7806 (tm) REVERT: A 269 ARG cc_start: 0.8371 (mtp85) cc_final: 0.8072 (mtp180) REVERT: A 593 ASP cc_start: 0.8208 (t0) cc_final: 0.7956 (t70) REVERT: A 654 GLN cc_start: 0.8136 (mt0) cc_final: 0.7725 (mt0) REVERT: A 679 ASP cc_start: 0.8463 (m-30) cc_final: 0.8142 (m-30) REVERT: A 842 ASP cc_start: 0.7785 (t0) cc_final: 0.7580 (t70) REVERT: A 847 GLU cc_start: 0.8098 (pm20) cc_final: 0.7818 (pm20) REVERT: B 17 TRP cc_start: 0.6497 (t-100) cc_final: 0.5951 (t60) outliers start: 23 outliers final: 6 residues processed: 131 average time/residue: 1.5973 time to fit residues: 226.3345 Evaluate side-chains 102 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 304 VAL 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 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 0.0060 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- 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 A 876 ASN B 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114223 restraints weight = 16778.626| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.26 r_work: 0.3285 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10933 Z= 0.132 Angle : 1.474 32.165 14845 Z= 0.543 Chirality : 0.144 1.872 1681 Planarity : 0.005 0.049 1869 Dihedral : 29.296 179.920 1961 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.20 % Allowed : 14.19 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1315 helix: 0.17 (0.22), residues: 561 sheet: -0.37 (0.39), residues: 153 loop : -1.59 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 392 HIS 0.002 0.001 HIS A 290 PHE 0.013 0.001 PHE A 922 TYR 0.023 0.001 TYR B 243 ARG 0.009 0.000 ARG A 893 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 2.90228 ( 6) link_BETA1-4 : bond 0.00146 ( 1) link_BETA1-4 : angle 1.97999 ( 3) hydrogen bonds : bond 0.04147 ( 437) hydrogen bonds : angle 4.30206 ( 1242) SS BOND : bond 0.00816 ( 5) SS BOND : angle 1.73560 ( 10) covalent geometry : bond 0.00307 (10925) covalent geometry : angle 1.47318 (14826) *********************** 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 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.854 Fit side-chains REVERT: A 170 LEU cc_start: 0.8158 (mt) cc_final: 0.7751 (tm) REVERT: A 192 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: A 269 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8071 (mtp180) REVERT: A 289 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7435 (pp20) REVERT: A 593 ASP cc_start: 0.8142 (t0) cc_final: 0.7866 (t70) REVERT: A 654 GLN cc_start: 0.8169 (mt0) cc_final: 0.7787 (mt0) REVERT: A 679 ASP cc_start: 0.8528 (m-30) cc_final: 0.8214 (m-30) REVERT: A 852 MET cc_start: 0.8706 (mmm) cc_final: 0.8487 (mmm) REVERT: A 954 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8842 (tp) REVERT: B 17 TRP cc_start: 0.6591 (t-100) cc_final: 0.6019 (t60) REVERT: B 126 CYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5396 (p) outliers start: 25 outliers final: 7 residues processed: 128 average time/residue: 1.5112 time to fit residues: 210.8304 Evaluate side-chains 107 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 576 VAL 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 142 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 83 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.144155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112019 restraints weight = 16464.416| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.38 r_work: 0.3249 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1930 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= 0.157 Angle : 1.484 32.037 14845 Z= 0.550 Chirality : 0.144 1.862 1681 Planarity : 0.005 0.050 1869 Dihedral : 29.207 179.757 1961 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.47 % Allowed : 15.59 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1315 helix: 0.38 (0.22), residues: 569 sheet: -0.20 (0.40), residues: 153 loop : -1.48 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 392 HIS 0.003 0.001 HIS A 290 PHE 0.018 0.002 PHE A 922 TYR 0.027 0.002 TYR B 243 ARG 0.006 0.000 ARG A 893 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 2) link_NAG-ASN : angle 2.99843 ( 6) link_BETA1-4 : bond 0.00055 ( 1) link_BETA1-4 : angle 2.09560 ( 3) hydrogen bonds : bond 0.04493 ( 437) hydrogen bonds : angle 4.27761 ( 1242) SS BOND : bond 0.00814 ( 5) SS BOND : angle 1.68148 ( 10) covalent geometry : bond 0.00382 (10925) covalent geometry : angle 1.48284 (14826) *********************** 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 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5060 (mtm-85) REVERT: A 91 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8665 (mtpp) REVERT: A 170 LEU cc_start: 0.8166 (mt) cc_final: 0.7742 (tm) REVERT: A 192 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: A 269 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8080 (mtp180) REVERT: A 289 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7462 (pp20) REVERT: A 418 TRP cc_start: 0.7395 (t-100) cc_final: 0.7039 (t-100) REVERT: A 593 ASP cc_start: 0.8168 (t0) cc_final: 0.7921 (t70) REVERT: A 654 GLN cc_start: 0.8170 (mt0) cc_final: 0.7799 (mt0) REVERT: A 679 ASP cc_start: 0.8456 (m-30) cc_final: 0.8117 (m-30) REVERT: B 17 TRP cc_start: 0.6585 (t-100) cc_final: 0.5993 (t60) REVERT: B 80 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7302 (tp) REVERT: B 126 CYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5560 (p) REVERT: B 177 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9047 (mp) outliers start: 28 outliers final: 11 residues processed: 128 average time/residue: 1.2661 time to fit residues: 174.8535 Evaluate side-chains 112 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 86 THR 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 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 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 122 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 B 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107626 restraints weight = 16524.505| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.78 r_work: 0.3280 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10933 Z= 0.145 Angle : 1.474 32.076 14845 Z= 0.544 Chirality : 0.144 1.855 1681 Planarity : 0.005 0.048 1869 Dihedral : 29.109 179.734 1961 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.56 % Allowed : 16.30 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1315 helix: 0.59 (0.23), residues: 570 sheet: -0.13 (0.40), residues: 155 loop : -1.33 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 418 HIS 0.003 0.001 HIS A 290 PHE 0.014 0.001 PHE A 922 TYR 0.025 0.001 TYR B 243 ARG 0.009 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 2) link_NAG-ASN : angle 2.90373 ( 6) link_BETA1-4 : bond 0.00030 ( 1) link_BETA1-4 : angle 1.91653 ( 3) hydrogen bonds : bond 0.04242 ( 437) hydrogen bonds : angle 4.20387 ( 1242) SS BOND : bond 0.00887 ( 5) SS BOND : angle 1.70457 ( 10) covalent geometry : bond 0.00349 (10925) covalent geometry : angle 1.47258 (14826) *********************** 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 138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5091 (mtm-85) REVERT: A 170 LEU cc_start: 0.8144 (mt) cc_final: 0.7750 (tm) REVERT: A 192 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 289 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7455 (pp20) REVERT: A 423 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6771 (ptp90) REVERT: A 479 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5686 (mp0) REVERT: A 593 ASP cc_start: 0.8120 (t0) cc_final: 0.7878 (t70) REVERT: A 654 GLN cc_start: 0.8102 (mt0) cc_final: 0.7722 (mt0) REVERT: A 679 ASP cc_start: 0.8414 (m-30) cc_final: 0.8094 (m-30) REVERT: B 17 TRP cc_start: 0.6535 (t-100) cc_final: 0.5961 (t60) REVERT: B 80 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7299 (tp) REVERT: B 126 CYS cc_start: 0.6149 (OUTLIER) cc_final: 0.5566 (p) REVERT: B 177 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9004 (mp) REVERT: B 268 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7482 (mtt) outliers start: 29 outliers final: 11 residues processed: 132 average time/residue: 1.3381 time to fit residues: 190.7010 Evaluate side-chains 115 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 86 THR 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 653 SER 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 Chi-restraints excluded: chain B residue 268 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 539 GLN A 540 ASN A 677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106786 restraints weight = 16606.128| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.77 r_work: 0.3260 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10933 Z= 0.162 Angle : 1.482 32.020 14845 Z= 0.550 Chirality : 0.144 1.863 1681 Planarity : 0.005 0.049 1869 Dihedral : 29.110 179.901 1961 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.08 % Allowed : 16.74 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1315 helix: 0.63 (0.23), residues: 570 sheet: -0.10 (0.40), residues: 155 loop : -1.29 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 418 HIS 0.003 0.001 HIS A 290 PHE 0.017 0.002 PHE A 922 TYR 0.027 0.002 TYR B 243 ARG 0.008 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 2) link_NAG-ASN : angle 2.98935 ( 6) link_BETA1-4 : bond 0.00079 ( 1) link_BETA1-4 : angle 1.99099 ( 3) hydrogen bonds : bond 0.04473 ( 437) hydrogen bonds : angle 4.23973 ( 1242) SS BOND : bond 0.00842 ( 5) SS BOND : angle 1.74419 ( 10) covalent geometry : bond 0.00396 (10925) covalent geometry : angle 1.48091 (14826) *********************** 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 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.5091 (mtm-85) REVERT: A 170 LEU cc_start: 0.8148 (mt) cc_final: 0.7766 (tm) REVERT: A 192 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: A 289 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7446 (pp20) REVERT: A 423 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6762 (ptp90) REVERT: A 593 ASP cc_start: 0.8118 (t0) cc_final: 0.7869 (t70) REVERT: A 654 GLN cc_start: 0.8120 (mt0) cc_final: 0.7902 (mt0) REVERT: A 679 ASP cc_start: 0.8426 (m-30) cc_final: 0.8125 (m-30) REVERT: A 954 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8821 (tp) REVERT: B 17 TRP cc_start: 0.6550 (t-100) cc_final: 0.5983 (t60) REVERT: B 80 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7306 (tp) REVERT: B 126 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5518 (p) REVERT: B 177 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9035 (mp) outliers start: 35 outliers final: 15 residues processed: 126 average time/residue: 1.2680 time to fit residues: 172.7850 Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 86 THR 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 480 ILE 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 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 142 GLU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 192 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 104 optimal weight: 0.3980 chunk 66 optimal weight: 0.0000 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110144 restraints weight = 16780.096| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.80 r_work: 0.3314 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 10933 Z= 0.108 Angle : 1.451 32.326 14845 Z= 0.529 Chirality : 0.144 1.862 1681 Planarity : 0.004 0.045 1869 Dihedral : 28.911 179.325 1961 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.56 % Allowed : 17.36 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1315 helix: 1.08 (0.23), residues: 560 sheet: -0.02 (0.40), residues: 155 loop : -1.12 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.002 0.001 HIS A 493 PHE 0.017 0.001 PHE B 139 TYR 0.015 0.001 TYR B 243 ARG 0.009 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 2) link_NAG-ASN : angle 2.61399 ( 6) link_BETA1-4 : bond 0.00013 ( 1) link_BETA1-4 : angle 1.66236 ( 3) hydrogen bonds : bond 0.03300 ( 437) hydrogen bonds : angle 4.02361 ( 1242) SS BOND : bond 0.00615 ( 5) SS BOND : angle 1.42781 ( 10) covalent geometry : bond 0.00249 (10925) covalent geometry : angle 1.45057 (14826) *********************** 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 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5103 (mtm-85) REVERT: A 170 LEU cc_start: 0.8136 (mt) cc_final: 0.7748 (tm) REVERT: A 183 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 192 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 198 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6603 (ttm170) REVERT: A 289 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7344 (pp20) REVERT: A 418 TRP cc_start: 0.7640 (t-100) cc_final: 0.7222 (t-100) REVERT: A 423 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6825 (ptp90) REVERT: A 427 LEU cc_start: 0.7612 (mt) cc_final: 0.7406 (mm) REVERT: A 593 ASP cc_start: 0.8077 (t0) cc_final: 0.7870 (t70) REVERT: A 654 GLN cc_start: 0.8052 (mt0) cc_final: 0.7660 (mt0) REVERT: A 679 ASP cc_start: 0.8496 (m-30) cc_final: 0.8142 (m-30) REVERT: B 17 TRP cc_start: 0.6649 (t-100) cc_final: 0.6087 (t60) REVERT: B 126 CYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5563 (p) outliers start: 29 outliers final: 10 residues processed: 131 average time/residue: 1.6911 time to fit residues: 237.9247 Evaluate side-chains 111 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 423 ARG Chi-restraints excluded: chain A residue 480 ILE 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 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 192 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.143939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106870 restraints weight = 16569.042| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.77 r_work: 0.3257 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10933 Z= 0.176 Angle : 1.492 31.873 14845 Z= 0.557 Chirality : 0.145 1.888 1681 Planarity : 0.005 0.050 1869 Dihedral : 28.985 179.678 1961 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.38 % Allowed : 18.15 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1315 helix: 0.81 (0.23), residues: 570 sheet: -0.03 (0.40), residues: 155 loop : -1.12 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 894 HIS 0.003 0.001 HIS A 290 PHE 0.026 0.002 PHE A 585 TYR 0.025 0.002 TYR B 243 ARG 0.008 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 2) link_NAG-ASN : angle 2.90572 ( 6) link_BETA1-4 : bond 0.00092 ( 1) link_BETA1-4 : angle 1.91311 ( 3) hydrogen bonds : bond 0.04465 ( 437) hydrogen bonds : angle 4.26017 ( 1242) SS BOND : bond 0.00640 ( 5) SS BOND : angle 3.73742 ( 10) covalent geometry : bond 0.00442 (10925) covalent geometry : angle 1.48831 (14826) *********************** 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 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5069 (mtm-85) REVERT: A 170 LEU cc_start: 0.8127 (mt) cc_final: 0.7699 (tm) REVERT: A 192 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: A 198 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6680 (ttm170) REVERT: A 289 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7346 (pp20) REVERT: A 418 TRP cc_start: 0.7573 (t-100) cc_final: 0.7110 (t-100) REVERT: A 423 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6914 (ptp90) REVERT: A 427 LEU cc_start: 0.7746 (mt) cc_final: 0.7484 (mm) REVERT: A 593 ASP cc_start: 0.8115 (t0) cc_final: 0.7882 (t70) REVERT: A 654 GLN cc_start: 0.8143 (mt0) cc_final: 0.7927 (mt0) REVERT: A 679 ASP cc_start: 0.8449 (m-30) cc_final: 0.8134 (m-30) REVERT: A 847 GLU cc_start: 0.8251 (pm20) cc_final: 0.8016 (pm20) REVERT: B 17 TRP cc_start: 0.6561 (t-100) cc_final: 0.5998 (t60) REVERT: B 126 CYS cc_start: 0.5973 (OUTLIER) cc_final: 0.5457 (p) outliers start: 27 outliers final: 13 residues processed: 120 average time/residue: 1.5527 time to fit residues: 202.9067 Evaluate side-chains 111 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 284 ILE 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 589 ILE Chi-restraints excluded: chain A residue 653 SER 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 142 GLU Chi-restraints excluded: chain B residue 192 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 76 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 118 optimal weight: 0.0870 chunk 103 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108754 restraints weight = 16690.451| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.79 r_work: 0.3298 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10933 Z= 0.124 Angle : 1.466 32.087 14845 Z= 0.539 Chirality : 0.145 1.861 1681 Planarity : 0.005 0.045 1869 Dihedral : 28.903 179.626 1961 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.85 % Allowed : 18.94 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1315 helix: 0.96 (0.23), residues: 572 sheet: -0.00 (0.40), residues: 155 loop : -1.05 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 392 HIS 0.003 0.001 HIS A 493 PHE 0.014 0.001 PHE B 139 TYR 0.017 0.001 TYR B 243 ARG 0.008 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 2) link_NAG-ASN : angle 2.71346 ( 6) link_BETA1-4 : bond 0.00190 ( 1) link_BETA1-4 : angle 1.72268 ( 3) hydrogen bonds : bond 0.03660 ( 437) hydrogen bonds : angle 4.15091 ( 1242) SS BOND : bond 0.00521 ( 5) SS BOND : angle 2.62520 ( 10) covalent geometry : bond 0.00299 (10925) covalent geometry : angle 1.46366 (14826) *********************** 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 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5899 (OUTLIER) cc_final: 0.5113 (mtm-85) REVERT: A 170 LEU cc_start: 0.8133 (mt) cc_final: 0.7731 (tm) REVERT: A 183 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7787 (mm-30) REVERT: A 192 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: A 198 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6619 (ttm170) REVERT: A 289 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7373 (pp20) REVERT: A 418 TRP cc_start: 0.7484 (t-100) cc_final: 0.7096 (t-100) REVERT: A 427 LEU cc_start: 0.7700 (mt) cc_final: 0.7474 (mm) REVERT: A 654 GLN cc_start: 0.8090 (mt0) cc_final: 0.7890 (mt0) REVERT: A 679 ASP cc_start: 0.8481 (m-30) cc_final: 0.8153 (m-30) REVERT: A 847 GLU cc_start: 0.8282 (pm20) cc_final: 0.8070 (pm20) REVERT: B 17 TRP cc_start: 0.6588 (t-100) cc_final: 0.6011 (t60) REVERT: B 126 CYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5655 (p) outliers start: 21 outliers final: 10 residues processed: 117 average time/residue: 1.2749 time to fit residues: 161.6570 Evaluate side-chains 108 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 284 ILE 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 653 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.144759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107647 restraints weight = 16662.532| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.79 r_work: 0.3268 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10933 Z= 0.145 Angle : 1.474 31.956 14845 Z= 0.545 Chirality : 0.145 1.886 1681 Planarity : 0.005 0.050 1869 Dihedral : 28.910 179.657 1961 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.15 % Allowed : 19.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1315 helix: 0.93 (0.23), residues: 570 sheet: -0.02 (0.41), residues: 155 loop : -1.03 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 392 HIS 0.002 0.001 HIS A 290 PHE 0.015 0.001 PHE A 922 TYR 0.024 0.001 TYR B 243 ARG 0.008 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 2) link_NAG-ASN : angle 2.82928 ( 6) link_BETA1-4 : bond 0.00065 ( 1) link_BETA1-4 : angle 1.84786 ( 3) hydrogen bonds : bond 0.04139 ( 437) hydrogen bonds : angle 4.21153 ( 1242) SS BOND : bond 0.00754 ( 5) SS BOND : angle 2.68160 ( 10) covalent geometry : bond 0.00358 (10925) covalent geometry : angle 1.47227 (14826) ********************** 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 110 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.5121 (mtm-85) REVERT: A 170 LEU cc_start: 0.8004 (mt) cc_final: 0.7664 (tm) REVERT: A 289 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7330 (pp20) REVERT: A 418 TRP cc_start: 0.7497 (t-100) cc_final: 0.7084 (t-100) REVERT: A 654 GLN cc_start: 0.8120 (mt0) cc_final: 0.7887 (mt0) REVERT: A 679 ASP cc_start: 0.8463 (m-30) cc_final: 0.8127 (m-30) REVERT: B 17 TRP cc_start: 0.6508 (t-100) cc_final: 0.5990 (t60) REVERT: B 126 CYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5596 (p) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 1.3269 time to fit residues: 156.5097 Evaluate side-chains 102 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 ILE 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 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 192 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108739 restraints weight = 16591.190| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.78 r_work: 0.3283 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 0.075 10933 Z= 0.124 Angle : 1.462 32.063 14845 Z= 0.537 Chirality : 0.145 1.864 1681 Planarity : 0.004 0.048 1869 Dihedral : 28.878 179.363 1961 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.67 % Allowed : 19.30 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1315 helix: 1.04 (0.23), residues: 572 sheet: -0.02 (0.41), residues: 155 loop : -0.99 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 392 HIS 0.002 0.001 HIS A 290 PHE 0.011 0.001 PHE A 291 TYR 0.018 0.001 TYR B 243 ARG 0.008 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 2) link_NAG-ASN : angle 2.69202 ( 6) link_BETA1-4 : bond 0.00050 ( 1) link_BETA1-4 : angle 1.70824 ( 3) hydrogen bonds : bond 0.03687 ( 437) hydrogen bonds : angle 4.14296 ( 1242) SS BOND : bond 0.00658 ( 5) SS BOND : angle 2.48543 ( 10) covalent geometry : bond 0.00300 (10925) covalent geometry : angle 1.46034 (14826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10369.68 seconds wall clock time: 185 minutes 44.01 seconds (11144.01 seconds total)