Starting phenix.real_space_refine on Sat Jun 21 21:00:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybn_33727/06_2025/7ybn_33727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybn_33727/06_2025/7ybn_33727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybn_33727/06_2025/7ybn_33727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybn_33727/06_2025/7ybn_33727.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybn_33727/06_2025/7ybn_33727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybn_33727/06_2025/7ybn_33727.cif" } resolution = 3.82 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= 0.004 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 16182 2.51 5 N 4200 2.21 5 O 4807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25301 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8439 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 55, 'TRANS': 1023} Chain breaks: 6 Chain: "B" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8434 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1021} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8428 Classifications: {'peptide': 1076} Link IDs: {'PTRANS': 56, 'TRANS': 1019} Chain breaks: 6 Time building chain proxies: 16.44, per 1000 atoms: 0.65 Number of scatterers: 25301 At special positions: 0 Unit cell: (146.59, 143.38, 220.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4807 8.00 N 4200 7.00 C 16182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.04 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 3.4 seconds 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6044 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 41 sheets defined 26.3% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.599A pdb=" N GLU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.806A pdb=" N VAL A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.214A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.623A pdb=" N LEU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.858A pdb=" N GLU A 617 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 618 " --> pdb=" O CYS A 615 " (cutoff:3.500A) Proline residue: A 619 - end of helix No H-bonds generated for 'chain 'A' and resid 614 through 621' Processing helix chain 'A' and resid 735 through 741 removed outlier: 3.771A pdb=" N TYR A 739 " --> pdb=" O ASP A 735 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 741 " --> pdb=" O THR A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.618A pdb=" N LEU A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.571A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 777 " --> pdb=" O ASP A 773 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.898A pdb=" N LEU A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.508A pdb=" N PHE A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.835A pdb=" N ALA A 869 " --> pdb=" O ASP A 865 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 873 " --> pdb=" O ALA A 869 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 4.329A pdb=" N ALA A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.749A pdb=" N MET A 900 " --> pdb=" O PHE A 896 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 908 removed outlier: 3.551A pdb=" N GLY A 908 " --> pdb=" O ASN A 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 905 through 908' Processing helix chain 'A' and resid 911 through 917 removed outlier: 4.059A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.591A pdb=" N ILE A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.714A pdb=" N VAL A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 963 " --> pdb=" O THR A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.950A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 3.787A pdb=" N VAL A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A1000 " --> pdb=" O THR A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1158 removed outlier: 4.617A pdb=" N GLU A1142 " --> pdb=" O PRO A1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.182A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.528A pdb=" N LEU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 5.130A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 409 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.981A pdb=" N THR B 636 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.567A pdb=" N SER B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 749 " --> pdb=" O THR B 745 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.581A pdb=" N ILE B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 774 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 4.269A pdb=" N LEU B 819 " --> pdb=" O PHE B 815 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 820 " --> pdb=" O ILE B 816 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.662A pdb=" N TYR B 871 " --> pdb=" O MET B 867 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 881 " --> pdb=" O ALA B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 905 removed outlier: 3.663A pdb=" N MET B 900 " --> pdb=" O PHE B 896 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 908 No H-bonds generated for 'chain 'B' and resid 906 through 908' Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.733A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.592A pdb=" N GLY B 930 " --> pdb=" O ASN B 926 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.749A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 961 " --> pdb=" O LEU B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.556A pdb=" N LEU B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1030 removed outlier: 4.515A pdb=" N GLU B 988 " --> pdb=" O LYS B 984 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL B 989 " --> pdb=" O VAL B 985 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR B1005 " --> pdb=" O SER B1001 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B1008 " --> pdb=" O THR B1004 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B1015 " --> pdb=" O ILE B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1159 removed outlier: 3.950A pdb=" N GLU B1142 " --> pdb=" O PRO B1138 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B1159 " --> pdb=" O LYS B1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 362 through 369 removed outlier: 4.612A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.964A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.883A pdb=" N ASN C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 628 through 636 removed outlier: 5.678A pdb=" N VAL C 633 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR C 634 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.953A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 864 through 882 removed outlier: 3.661A pdb=" N THR C 872 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 873 " --> pdb=" O ALA C 869 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 removed outlier: 4.107A pdb=" N ALA C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.797A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.729A pdb=" N GLY C 930 " --> pdb=" O ASN C 926 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 931 " --> pdb=" O SER C 927 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 932 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 942 No H-bonds generated for 'chain 'C' and resid 940 through 942' Processing helix chain 'C' and resid 943 through 963 removed outlier: 4.803A pdb=" N VAL C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 961 " --> pdb=" O LEU C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.547A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 1030 removed outlier: 3.892A pdb=" N ASP C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C1002 " --> pdb=" O ARG C 998 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C1019 " --> pdb=" O GLU C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1157 removed outlier: 3.841A pdb=" N GLU C1142 " --> pdb=" O PRO C1138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C1145 " --> pdb=" O PRO C1141 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C1146 " --> pdb=" O GLU C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.037A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.998A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.614A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.560A pdb=" N THR A 597 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 610 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 647 " --> pdb=" O TYR A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 326 removed outlier: 5.881A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 3.698A pdb=" N ASN A 352 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 397 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA9, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.322A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 725 removed outlier: 3.560A pdb=" N GLU A 723 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A1054 " --> pdb=" O GLY A1057 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 3.605A pdb=" N SER A1121 " --> pdb=" O ALA A1085 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS A1080 " --> pdb=" O VAL A1131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.921A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 262 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.780A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.186A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.616A pdb=" N THR B 597 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 322 through 326 removed outlier: 4.215A pdb=" N GLU B 322 " --> pdb=" O CYS B 536 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 324 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 541 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 322 through 326 removed outlier: 4.215A pdb=" N GLU B 322 " --> pdb=" O CYS B 536 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 324 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 548 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 573 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 352 through 356 removed outlier: 3.672A pdb=" N VAL B 393 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN B 392 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU B 514 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 376 " --> pdb=" O VAL B 431 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC4, first strand: chain 'B' and resid 471 through 472 removed outlier: 3.835A pdb=" N TYR B 471 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 487 " --> pdb=" O TYR B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.914A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 709 through 713 removed outlier: 3.585A pdb=" N LYS B1071 " --> pdb=" O ILE B 712 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 716 through 726 removed outlier: 3.716A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 716 through 726 removed outlier: 3.542A pdb=" N ALA B1054 " --> pdb=" O GLY B1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.379A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 3.565A pdb=" N VAL B1092 " --> pdb=" O THR B1103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B1103 " --> pdb=" O VAL B1092 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.851A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 63 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA C 262 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.145A pdb=" N ASP C 53 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 309 through 317 removed outlier: 3.860A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 323 through 326 removed outlier: 3.639A pdb=" N GLY C 548 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AD8, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.898A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE1, first strand: chain 'C' and resid 640 through 642 Processing sheet with id=AE2, first strand: chain 'C' and resid 652 through 653 removed outlier: 5.822A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 668 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.504A pdb=" N GLN C1069 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE C 716 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE C 718 " --> pdb=" O TYR C1065 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR C1065 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 720 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C1063 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C 722 " --> pdb=" O LEU C1061 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C1061 " --> pdb=" O THR C 722 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE C 724 " --> pdb=" O VAL C1059 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C1059 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C1057 " --> pdb=" O PRO C 726 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C1054 " --> pdb=" O GLY C1057 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1045 through 1048 removed outlier: 7.041A pdb=" N VAL C1063 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1118 through 1123 removed outlier: 3.862A pdb=" N ALA C1085 " --> pdb=" O SER C1121 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS C1080 " --> pdb=" O VAL C1131 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2517 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: 11.05 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7184 1.33 - 1.46: 4931 1.46 - 1.58: 13639 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 25896 Sorted by residual: bond pdb=" N PRO B 940 " pdb=" CD PRO B 940 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO C 897 " pdb=" CD PRO C 897 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO A 940 " pdb=" CD PRO A 940 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N PRO A 897 " pdb=" CD PRO A 897 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" N PRO B 897 " pdb=" CD PRO B 897 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.46e+01 ... (remaining 25891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 34900 2.56 - 5.11: 293 5.11 - 7.67: 20 7.67 - 10.23: 6 10.23 - 12.78: 10 Bond angle restraints: 35229 Sorted by residual: angle pdb=" CA PRO B 940 " pdb=" N PRO B 940 " pdb=" CD PRO B 940 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.34e+01 angle pdb=" CA PRO C 897 " pdb=" N PRO C 897 " pdb=" CD PRO C 897 " ideal model delta sigma weight residual 112.00 99.26 12.74 1.40e+00 5.10e-01 8.28e+01 angle pdb=" CA PRO A 940 " pdb=" N PRO A 940 " pdb=" CD PRO A 940 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.25e+01 angle pdb=" CA PRO A 897 " pdb=" N PRO A 897 " pdb=" CD PRO A 897 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" CA PRO B 897 " pdb=" N PRO B 897 " pdb=" CD PRO B 897 " ideal model delta sigma weight residual 112.00 99.40 12.60 1.40e+00 5.10e-01 8.10e+01 ... (remaining 35224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 13994 18.08 - 36.16: 1137 36.16 - 54.24: 207 54.24 - 72.32: 47 72.32 - 90.40: 34 Dihedral angle restraints: 15419 sinusoidal: 6024 harmonic: 9395 Sorted by residual: dihedral pdb=" CB CYS A 334 " pdb=" SG CYS A 334 " pdb=" SG CYS A 359 " pdb=" CB CYS A 359 " ideal model delta sinusoidal sigma weight residual 93.00 24.83 68.17 1 1.00e+01 1.00e-02 6.03e+01 dihedral pdb=" CB CYS B 736 " pdb=" SG CYS B 736 " pdb=" SG CYS B 758 " pdb=" CB CYS B 758 " ideal model delta sinusoidal sigma weight residual -86.00 -148.70 62.70 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual 93.00 30.64 62.36 1 1.00e+01 1.00e-02 5.15e+01 ... (remaining 15416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3178 0.050 - 0.100: 650 0.100 - 0.150: 140 0.150 - 0.200: 7 0.200 - 0.251: 2 Chirality restraints: 3977 Sorted by residual: chirality pdb=" CA VAL C 618 " pdb=" N VAL C 618 " pdb=" C VAL C 618 " pdb=" CB VAL C 618 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LEU A 241 " pdb=" N LEU A 241 " pdb=" C LEU A 241 " pdb=" CB LEU A 241 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LEU A 820 " pdb=" N LEU A 820 " pdb=" C LEU A 820 " pdb=" CB LEU A 820 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 3974 not shown) Planarity restraints: 4569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 896 " 0.115 5.00e-02 4.00e+02 1.62e-01 4.19e+01 pdb=" N PRO C 897 " -0.279 5.00e-02 4.00e+02 pdb=" CA PRO C 897 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO C 897 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 896 " -0.111 5.00e-02 4.00e+02 1.56e-01 3.87e+01 pdb=" N PRO A 897 " 0.268 5.00e-02 4.00e+02 pdb=" CA PRO A 897 " -0.081 5.00e-02 4.00e+02 pdb=" CD PRO A 897 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 889 " 0.106 5.00e-02 4.00e+02 1.49e-01 3.57e+01 pdb=" N PRO C 890 " -0.258 5.00e-02 4.00e+02 pdb=" CA PRO C 890 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO C 890 " 0.074 5.00e-02 4.00e+02 ... (remaining 4566 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 67 2.40 - 3.02: 14327 3.02 - 3.65: 36908 3.65 - 4.27: 52054 4.27 - 4.90: 88470 Nonbonded interactions: 191826 Sorted by model distance: nonbonded pdb=" CZ PHE A 18 " pdb=" CE1 PHE A 140 " model vdw 1.771 3.640 nonbonded pdb=" CE2 PHE C 18 " pdb=" CE1 PHE C 140 " model vdw 1.810 3.640 nonbonded pdb=" CZ PHE C 18 " pdb=" CZ PHE C 140 " model vdw 2.111 3.640 nonbonded pdb=" OG1 THR C 391 " pdb=" OE2 GLU C 514 " model vdw 2.118 3.040 nonbonded pdb=" O ASP A 288 " pdb=" OG SER A 295 " model vdw 2.126 3.040 ... (remaining 191821 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 620 or resid 639 through 825 or resid 853 throu \ gh 1160)) selection = (chain 'B' and (resid 14 through 620 or resid 639 through 825 or resid 853 throu \ gh 1160)) selection = (chain 'C' and (resid 14 through 620 or resid 639 through 1160)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.320 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.120 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.003 0.059 25932 Z= 0.175 Angle : 0.614 12.782 35301 Z= 0.358 Chirality : 0.043 0.251 3977 Planarity : 0.007 0.162 4569 Dihedral : 13.960 90.404 9267 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 0.71 % Allowed : 0.49 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.14), residues: 3190 helix: -0.37 (0.20), residues: 669 sheet: -0.10 (0.21), residues: 658 loop : -1.36 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 256 HIS 0.005 0.001 HIS C 517 PHE 0.032 0.001 PHE B 157 TYR 0.015 0.001 TYR A 349 ARG 0.006 0.000 ARG B 981 Details of bonding type rmsd hydrogen bonds : bond 0.29222 ( 912) hydrogen bonds : angle 9.05406 ( 2517) SS BOND : bond 0.00250 ( 36) SS BOND : angle 0.93030 ( 72) covalent geometry : bond 0.00277 (25896) covalent geometry : angle 0.61269 (35229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 2.770 Fit side-chains REVERT: A 588 CYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5890 (m) REVERT: C 366 LEU cc_start: 0.7074 (mp) cc_final: 0.6627 (mp) REVERT: C 631 TRP cc_start: 0.4727 (OUTLIER) cc_final: 0.4056 (m100) REVERT: C 639 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7553 (p0) REVERT: C 656 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6893 (p0) outliers start: 20 outliers final: 5 residues processed: 250 average time/residue: 0.3395 time to fit residues: 141.4081 Evaluate side-chains 163 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 656 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 291 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 137 ASN C 207 HIS C 656 ASN C1086 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.125757 restraints weight = 52562.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127991 restraints weight = 132837.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.128380 restraints weight = 52444.990| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25932 Z= 0.163 Angle : 0.614 11.498 35301 Z= 0.322 Chirality : 0.046 0.167 3977 Planarity : 0.004 0.065 4569 Dihedral : 5.060 65.106 3470 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 1.02 % Allowed : 7.39 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.14), residues: 3190 helix: 0.05 (0.19), residues: 731 sheet: -0.00 (0.20), residues: 683 loop : -1.43 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.004 0.001 HIS C1056 PHE 0.026 0.002 PHE B 560 TYR 0.021 0.001 TYR B1065 ARG 0.005 0.001 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.06529 ( 912) hydrogen bonds : angle 6.13020 ( 2517) SS BOND : bond 0.00367 ( 36) SS BOND : angle 1.15765 ( 72) covalent geometry : bond 0.00374 (25896) covalent geometry : angle 0.61219 (35229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 2.952 Fit side-chains revert: symmetry clash REVERT: A 588 CYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5831 (m) REVERT: A 826 LEU cc_start: 0.7408 (pp) cc_final: 0.7196 (mp) REVERT: B 425 ASP cc_start: 0.6129 (p0) cc_final: 0.5649 (p0) REVERT: B 750 LEU cc_start: 0.7806 (mp) cc_final: 0.7443 (tp) REVERT: C 545 THR cc_start: 0.8451 (t) cc_final: 0.8129 (p) REVERT: C 1027 MET cc_start: 0.9091 (tpp) cc_final: 0.8279 (ttm) outliers start: 29 outliers final: 16 residues processed: 207 average time/residue: 0.3320 time to fit residues: 114.8930 Evaluate side-chains 170 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 44 optimal weight: 0.0060 chunk 20 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 78 optimal weight: 0.0470 overall best weight: 2.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123771 restraints weight = 52345.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120789 restraints weight = 91519.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119269 restraints weight = 80813.450| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25932 Z= 0.196 Angle : 0.631 11.881 35301 Z= 0.328 Chirality : 0.046 0.166 3977 Planarity : 0.004 0.052 4569 Dihedral : 5.070 56.918 3464 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 1.98 % Allowed : 10.71 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.14), residues: 3190 helix: 0.09 (0.19), residues: 736 sheet: -0.09 (0.20), residues: 647 loop : -1.58 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.006 0.001 HIS B1056 PHE 0.024 0.002 PHE B 560 TYR 0.019 0.002 TYR A1065 ARG 0.005 0.001 ARG B1012 Details of bonding type rmsd hydrogen bonds : bond 0.06130 ( 912) hydrogen bonds : angle 5.78272 ( 2517) SS BOND : bond 0.00430 ( 36) SS BOND : angle 1.31651 ( 72) covalent geometry : bond 0.00464 (25896) covalent geometry : angle 0.62897 (35229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 2.749 Fit side-chains revert: symmetry clash REVERT: B 750 LEU cc_start: 0.7940 (mp) cc_final: 0.7578 (tp) REVERT: C 275 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7893 (mt) REVERT: C 876 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8824 (tt) REVERT: C 979 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 1027 MET cc_start: 0.9063 (tpp) cc_final: 0.8372 (ttm) outliers start: 56 outliers final: 36 residues processed: 208 average time/residue: 0.3167 time to fit residues: 113.1956 Evaluate side-chains 184 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 427 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 822 ASN Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 267 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 0.0000 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 504 GLN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.151196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125176 restraints weight = 52907.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127699 restraints weight = 126845.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127298 restraints weight = 49469.090| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25932 Z= 0.116 Angle : 0.551 9.998 35301 Z= 0.282 Chirality : 0.044 0.165 3977 Planarity : 0.004 0.046 4569 Dihedral : 4.553 57.921 3460 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 1.63 % Allowed : 13.39 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.14), residues: 3190 helix: 0.55 (0.20), residues: 731 sheet: -0.12 (0.20), residues: 664 loop : -1.41 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 104 HIS 0.006 0.001 HIS C 517 PHE 0.019 0.001 PHE B 560 TYR 0.021 0.001 TYR A 349 ARG 0.007 0.000 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 912) hydrogen bonds : angle 5.37741 ( 2517) SS BOND : bond 0.00256 ( 36) SS BOND : angle 0.96591 ( 72) covalent geometry : bond 0.00261 (25896) covalent geometry : angle 0.54936 (35229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 5.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 750 LEU cc_start: 0.7903 (mp) cc_final: 0.7550 (tp) REVERT: C 275 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7728 (mt) REVERT: C 1027 MET cc_start: 0.8982 (tpp) cc_final: 0.8314 (ttm) outliers start: 46 outliers final: 28 residues processed: 211 average time/residue: 0.3642 time to fit residues: 131.9367 Evaluate side-chains 182 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 427 PHE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 76 optimal weight: 0.0770 chunk 148 optimal weight: 0.1980 chunk 263 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.151239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.124867 restraints weight = 52766.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126779 restraints weight = 133747.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127483 restraints weight = 57947.673| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25932 Z= 0.115 Angle : 0.534 8.295 35301 Z= 0.275 Chirality : 0.043 0.169 3977 Planarity : 0.003 0.042 4569 Dihedral : 4.421 57.466 3460 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 2.37 % Allowed : 13.39 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.14), residues: 3190 helix: 0.86 (0.20), residues: 715 sheet: -0.10 (0.20), residues: 660 loop : -1.35 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.006 0.001 HIS C 517 PHE 0.048 0.001 PHE B 157 TYR 0.015 0.001 TYR B1065 ARG 0.002 0.000 ARG B 903 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 912) hydrogen bonds : angle 5.19947 ( 2517) SS BOND : bond 0.00259 ( 36) SS BOND : angle 0.92037 ( 72) covalent geometry : bond 0.00260 (25896) covalent geometry : angle 0.53264 (35229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.5759 (mmtt) cc_final: 0.5362 (mttp) REVERT: A 177 MET cc_start: -0.0552 (tpt) cc_final: -0.1879 (ttp) REVERT: B 750 LEU cc_start: 0.7853 (mp) cc_final: 0.7466 (tp) REVERT: B 952 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: C 275 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7823 (mt) REVERT: C 979 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 1027 MET cc_start: 0.8970 (tpp) cc_final: 0.8374 (ttm) outliers start: 67 outliers final: 43 residues processed: 218 average time/residue: 0.4241 time to fit residues: 156.4723 Evaluate side-chains 196 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 291 optimal weight: 4.9990 chunk 107 optimal weight: 40.0000 chunk 214 optimal weight: 30.0000 chunk 286 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 GLN B1000 GLN C 134 GLN C 933 GLN C1003 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.147196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.122707 restraints weight = 52768.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.120099 restraints weight = 82372.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119064 restraints weight = 60331.063| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25932 Z= 0.231 Angle : 0.652 8.611 35301 Z= 0.337 Chirality : 0.047 0.172 3977 Planarity : 0.004 0.044 4569 Dihedral : 4.943 57.128 3460 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 3.22 % Allowed : 13.85 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.14), residues: 3190 helix: 0.45 (0.19), residues: 716 sheet: -0.24 (0.20), residues: 663 loop : -1.55 (0.13), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 104 HIS 0.006 0.001 HIS B1056 PHE 0.032 0.002 PHE B 157 TYR 0.021 0.002 TYR A1065 ARG 0.003 0.001 ARG B 903 Details of bonding type rmsd hydrogen bonds : bond 0.05737 ( 912) hydrogen bonds : angle 5.52470 ( 2517) SS BOND : bond 0.00428 ( 36) SS BOND : angle 1.21627 ( 72) covalent geometry : bond 0.00552 (25896) covalent geometry : angle 0.64997 (35229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 153 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0320 (tpt) cc_final: -0.1690 (ttp) REVERT: A 338 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6335 (pp20) REVERT: A 378 TYR cc_start: 0.4730 (m-80) cc_final: 0.4398 (m-10) REVERT: A 459 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5081 (mp) REVERT: B 296 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: B 750 LEU cc_start: 0.8105 (mp) cc_final: 0.7782 (tp) REVERT: C 275 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7975 (mt) REVERT: C 871 TYR cc_start: 0.9249 (OUTLIER) cc_final: 0.8729 (m-10) REVERT: C 876 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8963 (tt) REVERT: C 979 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8333 (mp) REVERT: C 1027 MET cc_start: 0.9133 (tpp) cc_final: 0.8482 (ttm) REVERT: C 1157 HIS cc_start: 0.1121 (OUTLIER) cc_final: 0.0022 (t-170) outliers start: 91 outliers final: 65 residues processed: 229 average time/residue: 0.3812 time to fit residues: 149.0656 Evaluate side-chains 216 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 144 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 427 PHE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1157 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 193 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 642 GLN B1000 GLN C1003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123481 restraints weight = 52902.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120368 restraints weight = 77668.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118233 restraints weight = 57227.172| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25932 Z= 0.223 Angle : 0.642 8.472 35301 Z= 0.334 Chirality : 0.047 0.202 3977 Planarity : 0.004 0.046 4569 Dihedral : 5.013 51.075 3460 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 3.32 % Allowed : 14.59 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.14), residues: 3190 helix: 0.38 (0.19), residues: 718 sheet: -0.32 (0.20), residues: 644 loop : -1.64 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 104 HIS 0.006 0.001 HIS B1046 PHE 0.021 0.002 PHE B 541 TYR 0.025 0.002 TYR A 419 ARG 0.005 0.001 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.05684 ( 912) hydrogen bonds : angle 5.50686 ( 2517) SS BOND : bond 0.00414 ( 36) SS BOND : angle 1.51789 ( 72) covalent geometry : bond 0.00534 (25896) covalent geometry : angle 0.63907 (35229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 151 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0754 (tpt) cc_final: -0.2013 (ttp) REVERT: A 338 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6364 (pp20) REVERT: A 459 LEU cc_start: 0.5632 (OUTLIER) cc_final: 0.4909 (mp) REVERT: B 296 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: B 750 LEU cc_start: 0.8086 (mp) cc_final: 0.7743 (tp) REVERT: C 275 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8005 (mt) REVERT: C 871 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8711 (m-10) REVERT: C 876 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8974 (tt) REVERT: C 979 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8319 (mp) REVERT: C 1027 MET cc_start: 0.9148 (tpp) cc_final: 0.8514 (ttm) REVERT: C 1157 HIS cc_start: 0.1069 (OUTLIER) cc_final: -0.0022 (t-170) outliers start: 94 outliers final: 67 residues processed: 233 average time/residue: 0.3670 time to fit residues: 145.3199 Evaluate side-chains 210 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 427 PHE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1080 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1157 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 158 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 306 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.147704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123374 restraints weight = 52435.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120537 restraints weight = 81734.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.119324 restraints weight = 58005.426| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25932 Z= 0.168 Angle : 0.602 8.422 35301 Z= 0.310 Chirality : 0.045 0.179 3977 Planarity : 0.004 0.044 4569 Dihedral : 4.845 45.509 3459 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.11 % Rotamer: Outliers : 3.22 % Allowed : 15.27 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.14), residues: 3190 helix: 0.58 (0.19), residues: 717 sheet: -0.24 (0.20), residues: 633 loop : -1.62 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 104 HIS 0.004 0.001 HIS B1046 PHE 0.052 0.002 PHE B 157 TYR 0.018 0.001 TYR A 419 ARG 0.009 0.000 ARG C 317 Details of bonding type rmsd hydrogen bonds : bond 0.05208 ( 912) hydrogen bonds : angle 5.36793 ( 2517) SS BOND : bond 0.00317 ( 36) SS BOND : angle 1.24064 ( 72) covalent geometry : bond 0.00398 (25896) covalent geometry : angle 0.60009 (35229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 151 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0953 (tpt) cc_final: -0.2158 (ttp) REVERT: A 338 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6417 (pp20) REVERT: A 378 TYR cc_start: 0.4857 (m-80) cc_final: 0.4562 (m-10) REVERT: A 459 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.4921 (mp) REVERT: B 750 LEU cc_start: 0.8064 (mp) cc_final: 0.7736 (tp) REVERT: C 275 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7983 (mt) REVERT: C 871 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8657 (m-10) REVERT: C 876 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9042 (tt) REVERT: C 979 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8307 (mp) REVERT: C 1027 MET cc_start: 0.9078 (tpp) cc_final: 0.8468 (ttm) REVERT: C 1157 HIS cc_start: 0.1044 (OUTLIER) cc_final: 0.0029 (t-170) outliers start: 91 outliers final: 71 residues processed: 228 average time/residue: 0.3348 time to fit residues: 130.1951 Evaluate side-chains 220 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 143 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 427 PHE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1080 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1157 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 14 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 295 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 282 optimal weight: 0.8980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** 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 = 0.4025 r_free = 0.4025 target = 0.147504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123058 restraints weight = 53039.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120277 restraints weight = 83114.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118757 restraints weight = 63808.300| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25932 Z= 0.173 Angle : 0.604 8.820 35301 Z= 0.311 Chirality : 0.045 0.166 3977 Planarity : 0.004 0.044 4569 Dihedral : 4.812 39.956 3458 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.11 % Rotamer: Outliers : 3.07 % Allowed : 15.55 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.14), residues: 3190 helix: 0.62 (0.19), residues: 716 sheet: -0.29 (0.20), residues: 631 loop : -1.65 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.004 0.001 HIS B1046 PHE 0.027 0.002 PHE A 398 TYR 0.018 0.001 TYR A 419 ARG 0.004 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 912) hydrogen bonds : angle 5.35209 ( 2517) SS BOND : bond 0.00336 ( 36) SS BOND : angle 1.16089 ( 72) covalent geometry : bond 0.00411 (25896) covalent geometry : angle 0.60235 (35229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 146 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0972 (tpt) cc_final: -0.2140 (ttp) REVERT: A 338 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6374 (pp20) REVERT: A 378 TYR cc_start: 0.4943 (m-80) cc_final: 0.4639 (m-10) REVERT: A 459 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.4950 (mp) REVERT: B 296 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: B 750 LEU cc_start: 0.8086 (mp) cc_final: 0.7763 (tp) REVERT: C 275 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8002 (mt) REVERT: C 333 LEU cc_start: 0.7670 (mp) cc_final: 0.7330 (tt) REVERT: C 871 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8681 (m-10) REVERT: C 876 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9019 (tt) REVERT: C 979 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 1027 MET cc_start: 0.9098 (tpp) cc_final: 0.8496 (ttm) REVERT: C 1157 HIS cc_start: 0.1057 (OUTLIER) cc_final: 0.0162 (t-170) outliers start: 87 outliers final: 72 residues processed: 221 average time/residue: 0.4535 time to fit residues: 175.4319 Evaluate side-chains 218 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 139 time to evaluate : 6.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 427 PHE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1080 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1157 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 123 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 295 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 952 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.149970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125874 restraints weight = 52856.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127568 restraints weight = 133377.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126962 restraints weight = 51886.895| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25932 Z= 0.109 Angle : 0.555 11.191 35301 Z= 0.281 Chirality : 0.043 0.184 3977 Planarity : 0.004 0.044 4569 Dihedral : 4.412 39.395 3458 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 2.01 % Allowed : 16.82 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.15), residues: 3190 helix: 1.02 (0.20), residues: 716 sheet: -0.14 (0.20), residues: 646 loop : -1.51 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 104 HIS 0.004 0.001 HIS C 517 PHE 0.052 0.001 PHE B 157 TYR 0.013 0.001 TYR B1065 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 912) hydrogen bonds : angle 5.07773 ( 2517) SS BOND : bond 0.00240 ( 36) SS BOND : angle 0.99956 ( 72) covalent geometry : bond 0.00243 (25896) covalent geometry : angle 0.55330 (35229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1446 (tpt) cc_final: -0.2450 (ttp) REVERT: A 338 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6482 (pp20) REVERT: A 378 TYR cc_start: 0.4890 (m-80) cc_final: 0.4542 (m-10) REVERT: A 459 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.4885 (mp) REVERT: B 750 LEU cc_start: 0.7992 (mp) cc_final: 0.7716 (tp) REVERT: C 177 MET cc_start: 0.1989 (ptt) cc_final: -0.2210 (ttt) REVERT: C 275 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7816 (mt) REVERT: C 333 LEU cc_start: 0.7546 (mp) cc_final: 0.7239 (tt) REVERT: C 1027 MET cc_start: 0.9018 (tpp) cc_final: 0.8453 (ttm) outliers start: 57 outliers final: 47 residues processed: 209 average time/residue: 0.3127 time to fit residues: 113.3580 Evaluate side-chains 197 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 208 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.146628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123404 restraints weight = 52959.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119445 restraints weight = 78531.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117253 restraints weight = 57497.509| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25932 Z= 0.227 Angle : 0.652 10.746 35301 Z= 0.335 Chirality : 0.046 0.163 3977 Planarity : 0.004 0.043 4569 Dihedral : 4.773 25.556 3456 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 2.33 % Allowed : 16.40 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.23 (0.14), residues: 3190 helix: 0.63 (0.20), residues: 717 sheet: -0.29 (0.20), residues: 655 loop : -1.68 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.006 0.001 HIS B1046 PHE 0.022 0.002 PHE B 541 TYR 0.021 0.002 TYR A1065 ARG 0.004 0.001 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.05434 ( 912) hydrogen bonds : angle 5.38282 ( 2517) SS BOND : bond 0.00379 ( 36) SS BOND : angle 1.32015 ( 72) covalent geometry : bond 0.00546 (25896) covalent geometry : angle 0.65041 (35229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7806.48 seconds wall clock time: 142 minutes 15.53 seconds (8535.53 seconds total)