Starting phenix.real_space_refine on Thu Mar 5 20:38:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybn_33727/03_2026/7ybn_33727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybn_33727/03_2026/7ybn_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_33727/03_2026/7ybn_33727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybn_33727/03_2026/7ybn_33727.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybn_33727/03_2026/7ybn_33727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybn_33727/03_2026/7ybn_33727.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.28, per 1000 atoms: 0.21 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 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: 1.07 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: 5.27 Time building geometry restraints manager: 2.71 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.320 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- 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 : 9.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (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 ARG 0.006 0.000 ARG B 981 TYR 0.015 0.001 TYR A 349 PHE 0.032 0.001 PHE B 157 TRP 0.013 0.001 TRP C 256 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00277 (25896) covalent geometry : angle 0.61269 (35229) SS BOND : bond 0.00250 ( 36) SS BOND : angle 0.93030 ( 72) hydrogen bonds : bond 0.29222 ( 912) hydrogen bonds : angle 9.05406 ( 2517) *********************** 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 : 0.792 Fit side-chains revert: symmetry clash REVERT: A 588 CYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5887 (m) REVERT: C 366 LEU cc_start: 0.7074 (mp) cc_final: 0.6626 (mp) REVERT: C 631 TRP cc_start: 0.4727 (OUTLIER) cc_final: 0.4055 (m100) REVERT: C 639 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7555 (p0) REVERT: C 656 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6892 (p0) outliers start: 20 outliers final: 5 residues processed: 250 average time/residue: 0.1392 time to fit residues: 58.1314 Evaluate side-chains 165 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 125 ASN B 137 ASN C 207 HIS C 772 GLN C1086 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.152312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.127091 restraints weight = 52609.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.129218 restraints weight = 131870.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129009 restraints weight = 50342.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129292 restraints weight = 43163.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129864 restraints weight = 33005.644| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25932 Z= 0.150 Angle : 0.600 10.905 35301 Z= 0.315 Chirality : 0.045 0.166 3977 Planarity : 0.004 0.067 4569 Dihedral : 5.108 66.752 3470 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 1.02 % Allowed : 6.71 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3190 helix: 0.04 (0.19), residues: 744 sheet: 0.07 (0.20), residues: 680 loop : -1.45 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 455 TYR 0.019 0.001 TYR B1065 PHE 0.025 0.001 PHE B 560 TRP 0.021 0.001 TRP B 104 HIS 0.004 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00334 (25896) covalent geometry : angle 0.59850 (35229) SS BOND : bond 0.00389 ( 36) SS BOND : angle 1.09410 ( 72) hydrogen bonds : bond 0.06823 ( 912) hydrogen bonds : angle 6.18915 ( 2517) *********************** 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 : 0.636 Fit side-chains revert: symmetry clash REVERT: A 588 CYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5798 (m) REVERT: A 826 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7162 (mp) REVERT: B 425 ASP cc_start: 0.6278 (p0) cc_final: 0.5979 (p0) REVERT: B 750 LEU cc_start: 0.7824 (mp) cc_final: 0.7464 (tp) REVERT: C 545 THR cc_start: 0.8453 (t) cc_final: 0.8135 (p) REVERT: C 1027 MET cc_start: 0.9092 (tpp) cc_final: 0.8222 (ttm) outliers start: 29 outliers final: 15 residues processed: 207 average time/residue: 0.1362 time to fit residues: 47.1768 Evaluate side-chains 171 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 826 LEU 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 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 135 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 257 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 107 optimal weight: 40.0000 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.0070 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.149898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127452 restraints weight = 52921.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127852 restraints weight = 137953.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127707 restraints weight = 55366.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128030 restraints weight = 46610.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127989 restraints weight = 34545.617| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 25932 Z= 0.174 Angle : 0.609 12.071 35301 Z= 0.315 Chirality : 0.045 0.163 3977 Planarity : 0.004 0.048 4569 Dihedral : 4.948 55.263 3464 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 1.66 % Allowed : 10.35 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3190 helix: 0.22 (0.19), residues: 729 sheet: -0.01 (0.20), residues: 651 loop : -1.51 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 452 TYR 0.018 0.002 TYR A1065 PHE 0.023 0.002 PHE B 560 TRP 0.017 0.001 TRP B 104 HIS 0.006 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00414 (25896) covalent geometry : angle 0.60711 (35229) SS BOND : bond 0.00357 ( 36) SS BOND : angle 1.23639 ( 72) hydrogen bonds : bond 0.05890 ( 912) hydrogen bonds : angle 5.73687 ( 2517) *********************** 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 216 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 826 LEU cc_start: 0.7551 (pp) cc_final: 0.7266 (mp) REVERT: B 750 LEU cc_start: 0.7922 (mp) cc_final: 0.7568 (tp) REVERT: B 952 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: C 275 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7854 (mt) REVERT: C 979 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8224 (mp) REVERT: C 1027 MET cc_start: 0.9048 (tpp) cc_final: 0.8396 (ttm) outliers start: 47 outliers final: 28 residues processed: 206 average time/residue: 0.1346 time to fit residues: 47.5020 Evaluate side-chains 174 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 588 CYS Chi-restraints excluded: chain B residue 618 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 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 393 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 822 ASN Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 71 optimal weight: 0.2980 chunk 265 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.149041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.122793 restraints weight = 52451.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125287 restraints weight = 130354.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125438 restraints weight = 50882.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125692 restraints weight = 41339.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.126313 restraints weight = 32604.228| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25932 Z= 0.174 Angle : 0.600 10.286 35301 Z= 0.310 Chirality : 0.045 0.168 3977 Planarity : 0.004 0.043 4569 Dihedral : 4.784 56.610 3460 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 2.19 % Allowed : 12.93 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3190 helix: 0.35 (0.19), residues: 725 sheet: -0.13 (0.20), residues: 652 loop : -1.53 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1012 TYR 0.018 0.001 TYR A1065 PHE 0.020 0.002 PHE B 560 TRP 0.018 0.001 TRP B 104 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00412 (25896) covalent geometry : angle 0.59868 (35229) SS BOND : bond 0.00362 ( 36) SS BOND : angle 1.16156 ( 72) hydrogen bonds : bond 0.05501 ( 912) hydrogen bonds : angle 5.56428 ( 2517) *********************** 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 230 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4388 (tt) REVERT: A 177 MET cc_start: -0.0500 (tpt) cc_final: -0.1826 (ttp) REVERT: A 826 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7237 (mp) REVERT: B 750 LEU cc_start: 0.7972 (mp) cc_final: 0.7656 (tp) REVERT: C 275 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7854 (mt) REVERT: C 876 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8863 (tt) REVERT: C 979 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 1027 MET cc_start: 0.9048 (tpp) cc_final: 0.8402 (ttm) outliers start: 62 outliers final: 44 residues processed: 216 average time/residue: 0.1304 time to fit residues: 48.7317 Evaluate side-chains 200 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE 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 647 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL 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 203 ILE Chi-restraints excluded: chain B residue 210 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 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 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 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 545 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 977 ASP 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 1094 VAL Chi-restraints excluded: chain C residue 1103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 85 optimal weight: 0.0970 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125630 restraints weight = 52478.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122131 restraints weight = 82218.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121171 restraints weight = 59335.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120069 restraints weight = 62996.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118841 restraints weight = 61215.818| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2465 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= 0.139 Angle : 0.562 8.679 35301 Z= 0.291 Chirality : 0.044 0.162 3977 Planarity : 0.004 0.043 4569 Dihedral : 4.631 57.499 3460 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 2.65 % Allowed : 13.64 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3190 helix: 0.55 (0.20), residues: 726 sheet: -0.15 (0.20), residues: 668 loop : -1.49 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1012 TYR 0.016 0.001 TYR B1065 PHE 0.047 0.001 PHE B 157 TRP 0.020 0.001 TRP B 104 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00325 (25896) covalent geometry : angle 0.56058 (35229) SS BOND : bond 0.00307 ( 36) SS BOND : angle 1.03026 ( 72) hydrogen bonds : bond 0.04985 ( 912) hydrogen bonds : angle 5.34509 ( 2517) *********************** 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 242 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 167 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0349 (tpt) cc_final: -0.1723 (ttp) REVERT: A 826 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7248 (mp) REVERT: B 229 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6991 (mm) REVERT: B 750 LEU cc_start: 0.7977 (mp) cc_final: 0.7586 (tp) REVERT: C 275 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7913 (mt) REVERT: C 871 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: C 876 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8988 (tt) REVERT: C 1027 MET cc_start: 0.8948 (tpp) cc_final: 0.8262 (ttm) outliers start: 75 outliers final: 49 residues processed: 227 average time/residue: 0.1277 time to fit residues: 49.5023 Evaluate side-chains 203 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 761 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 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 229 LEU 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 718 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 788 LYS 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 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 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 427 PHE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 549 VAL 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 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 933 GLN Chi-restraints excluded: chain C residue 977 ASP 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 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 216 optimal weight: 0.0570 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 0.0570 chunk 43 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 542 ASN B1000 GLN C 134 GLN C1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.151094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126135 restraints weight = 53137.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128409 restraints weight = 132745.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127914 restraints weight = 48681.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128328 restraints weight = 41457.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128748 restraints weight = 31565.484| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2607 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 : 0.534 8.318 35301 Z= 0.274 Chirality : 0.043 0.160 3977 Planarity : 0.003 0.046 4569 Dihedral : 4.405 57.997 3460 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 14.73 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3190 helix: 0.92 (0.20), residues: 716 sheet: -0.09 (0.19), residues: 698 loop : -1.35 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.017 0.001 TYR A 419 PHE 0.021 0.001 PHE C 815 TRP 0.022 0.001 TRP B 104 HIS 0.006 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00242 (25896) covalent geometry : angle 0.53270 (35229) SS BOND : bond 0.00251 ( 36) SS BOND : angle 0.92398 ( 72) hydrogen bonds : bond 0.04405 ( 912) hydrogen bonds : angle 5.15047 ( 2517) *********************** 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 227 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0574 (tpt) cc_final: -0.1897 (ttp) REVERT: A 338 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6557 (pp20) REVERT: A 459 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.4903 (mp) REVERT: A 826 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7201 (mp) REVERT: B 750 LEU cc_start: 0.7961 (mp) cc_final: 0.7585 (tp) REVERT: B 952 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: C 275 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7807 (mt) REVERT: C 1027 MET cc_start: 0.8951 (tpp) cc_final: 0.8328 (ttm) REVERT: C 1157 HIS cc_start: 0.0654 (OUTLIER) cc_final: -0.0032 (t-170) outliers start: 65 outliers final: 42 residues processed: 218 average time/residue: 0.1386 time to fit residues: 51.0694 Evaluate side-chains 195 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 310 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 523 CYS 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 826 LEU 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 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 876 LEU 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 127 VAL 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 391 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL 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 820 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 977 ASP 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 1094 VAL 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 291 optimal weight: 3.9990 chunk 21 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 177 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 293 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.149435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.125334 restraints weight = 52506.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122207 restraints weight = 80203.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120168 restraints weight = 62148.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119587 restraints weight = 63784.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118544 restraints weight = 57413.178| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25932 Z= 0.147 Angle : 0.569 10.775 35301 Z= 0.290 Chirality : 0.044 0.164 3977 Planarity : 0.004 0.046 4569 Dihedral : 4.510 59.747 3459 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 2.65 % Allowed : 14.70 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3190 helix: 0.88 (0.20), residues: 716 sheet: -0.08 (0.20), residues: 678 loop : -1.41 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 271 TYR 0.032 0.001 TYR A 419 PHE 0.052 0.001 PHE B 157 TRP 0.021 0.001 TRP B 104 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00346 (25896) covalent geometry : angle 0.56752 (35229) SS BOND : bond 0.00316 ( 36) SS BOND : angle 1.04712 ( 72) hydrogen bonds : bond 0.04756 ( 912) hydrogen bonds : angle 5.19341 ( 2517) *********************** 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 228 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 153 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0633 (tpt) cc_final: -0.1947 (ttp) REVERT: A 338 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6515 (pp20) REVERT: A 378 TYR cc_start: 0.4773 (m-80) cc_final: 0.4371 (m-10) REVERT: A 459 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5069 (mp) REVERT: A 826 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7228 (mp) REVERT: B 750 LEU cc_start: 0.8001 (mp) cc_final: 0.7610 (tp) REVERT: B 952 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: C 275 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7846 (mt) REVERT: C 871 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8593 (m-10) REVERT: C 1027 MET cc_start: 0.8981 (tpp) cc_final: 0.8362 (ttm) REVERT: C 1157 HIS cc_start: 0.0726 (OUTLIER) cc_final: -0.0061 (t-170) outliers start: 75 outliers final: 56 residues processed: 217 average time/residue: 0.1325 time to fit residues: 50.0068 Evaluate side-chains 210 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 148 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 817 GLU Chi-restraints excluded: chain A residue 826 LEU 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 316 PHE 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 913 VAL Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1114 THR 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 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 703 VAL 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 909 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 977 ASP 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 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 254 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 190 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.145038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120733 restraints weight = 52660.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117897 restraints weight = 85329.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115762 restraints weight = 67728.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114713 restraints weight = 70502.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113610 restraints weight = 61930.838| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 25932 Z= 0.305 Angle : 0.728 9.399 35301 Z= 0.380 Chirality : 0.049 0.163 3977 Planarity : 0.005 0.047 4569 Dihedral : 5.334 50.637 3459 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 3.53 % Allowed : 14.49 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3190 helix: 0.15 (0.19), residues: 716 sheet: -0.36 (0.20), residues: 633 loop : -1.73 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 271 TYR 0.025 0.002 TYR A1065 PHE 0.041 0.003 PHE B 157 TRP 0.017 0.002 TRP A 351 HIS 0.009 0.002 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00732 (25896) covalent geometry : angle 0.72533 (35229) SS BOND : bond 0.00723 ( 36) SS BOND : angle 1.51080 ( 72) hydrogen bonds : bond 0.06406 ( 912) hydrogen bonds : angle 5.74685 ( 2517) *********************** 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 255 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 155 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0798 (tpt) cc_final: -0.2010 (ttp) REVERT: A 338 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6514 (pp20) REVERT: A 459 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4567 (mp) REVERT: A 743 ASP cc_start: 0.6721 (t0) cc_final: 0.6364 (t0) REVERT: A 826 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7303 (mt) REVERT: B 296 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: B 750 LEU cc_start: 0.8178 (mp) cc_final: 0.7873 (tp) REVERT: B 905 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.9090 (m-40) REVERT: C 275 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8081 (mt) REVERT: C 317 ARG cc_start: 0.6728 (ptp90) cc_final: 0.6309 (mmm160) REVERT: C 871 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.8852 (m-10) REVERT: C 1027 MET cc_start: 0.9240 (tpp) cc_final: 0.8599 (ttm) REVERT: C 1157 HIS cc_start: 0.0977 (OUTLIER) cc_final: -0.0066 (t-170) outliers start: 100 outliers final: 75 residues processed: 241 average time/residue: 0.1293 time to fit residues: 53.5519 Evaluate side-chains 221 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 139 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU 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 588 CYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 647 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 826 LEU 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 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 880 ILE Chi-restraints excluded: chain B residue 905 ASN 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 127 VAL Chi-restraints excluded: chain C residue 157 PHE 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 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 909 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 977 ASP 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 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 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 189 optimal weight: 0.6980 chunk 204 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 316 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 952 GLN B1000 GLN C 953 ASN C1003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.150260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125080 restraints weight = 52673.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127549 restraints weight = 131862.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127175 restraints weight = 48914.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127602 restraints weight = 41852.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128052 restraints weight = 31861.890| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25932 Z= 0.108 Angle : 0.568 10.169 35301 Z= 0.289 Chirality : 0.044 0.163 3977 Planarity : 0.004 0.062 4569 Dihedral : 4.541 43.032 3458 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 2.12 % Allowed : 16.18 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3190 helix: 0.91 (0.20), residues: 716 sheet: -0.11 (0.20), residues: 642 loop : -1.51 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 452 TYR 0.020 0.001 TYR A 419 PHE 0.036 0.001 PHE C 815 TRP 0.032 0.001 TRP B 104 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00230 (25896) covalent geometry : angle 0.56636 (35229) SS BOND : bond 0.00242 ( 36) SS BOND : angle 1.17403 ( 72) hydrogen bonds : bond 0.04499 ( 912) hydrogen bonds : angle 5.15629 ( 2517) *********************** 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 226 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: -0.1127 (tpt) cc_final: -0.2226 (ttp) REVERT: A 338 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6555 (pp20) REVERT: A 378 TYR cc_start: 0.4917 (m-80) cc_final: 0.4568 (m-10) REVERT: A 459 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.4764 (mp) REVERT: A 826 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 750 LEU cc_start: 0.7993 (mp) cc_final: 0.7695 (tp) REVERT: B 1092 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7895 (m) REVERT: C 317 ARG cc_start: 0.6491 (ptp90) cc_final: 0.6262 (tpt90) REVERT: C 1027 MET cc_start: 0.9066 (tpp) cc_final: 0.8358 (ttm) outliers start: 60 outliers final: 49 residues processed: 216 average time/residue: 0.1331 time to fit residues: 49.2839 Evaluate side-chains 204 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL 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 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 826 LEU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL 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 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 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 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE 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 427 PHE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 817 GLU 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 977 ASP 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 193 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 247 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 291 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.150874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123772 restraints weight = 52951.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125572 restraints weight = 135133.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.126755 restraints weight = 64962.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127045 restraints weight = 44367.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127840 restraints weight = 37185.561| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25932 Z= 0.100 Angle : 0.538 9.859 35301 Z= 0.272 Chirality : 0.043 0.207 3977 Planarity : 0.004 0.049 4569 Dihedral : 4.232 39.793 3458 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 1.73 % Allowed : 16.78 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3190 helix: 1.18 (0.20), residues: 716 sheet: -0.02 (0.20), residues: 646 loop : -1.41 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 401 TYR 0.016 0.001 TYR A 419 PHE 0.047 0.001 PHE B 157 TRP 0.027 0.001 TRP B 104 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00221 (25896) covalent geometry : angle 0.53699 (35229) SS BOND : bond 0.00246 ( 36) SS BOND : angle 0.90781 ( 72) hydrogen bonds : bond 0.04070 ( 912) hydrogen bonds : angle 4.99011 ( 2517) ********************** 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 213 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.882 Fit side-chains REVERT: A 177 MET cc_start: -0.1176 (tpt) cc_final: -0.2270 (ttp) REVERT: A 338 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6799 (pp20) REVERT: A 378 TYR cc_start: 0.4811 (m-80) cc_final: 0.4437 (m-10) REVERT: A 459 LEU cc_start: 0.5375 (OUTLIER) cc_final: 0.4858 (mp) REVERT: A 826 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7281 (mp) REVERT: B 750 LEU cc_start: 0.7978 (mp) cc_final: 0.7667 (tp) REVERT: B 952 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: B 1092 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7888 (m) REVERT: C 333 LEU cc_start: 0.7507 (mp) cc_final: 0.7291 (tt) REVERT: C 740 ILE cc_start: 0.9105 (pt) cc_final: 0.8862 (mt) REVERT: C 1027 MET cc_start: 0.8998 (tpp) cc_final: 0.8391 (ttm) REVERT: C 1029 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7178 (mp0) outliers start: 49 outliers final: 40 residues processed: 206 average time/residue: 0.1301 time to fit residues: 46.5366 Evaluate side-chains 191 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL 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 647 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL 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 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 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 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 817 GLU 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 977 ASP Chi-restraints excluded: chain C residue 1029 GLU 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 187 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 257 optimal weight: 0.4980 chunk 163 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 201 optimal weight: 0.0870 chunk 236 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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** B 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.127431 restraints weight = 52900.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129531 restraints weight = 130280.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128722 restraints weight = 50947.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129286 restraints weight = 43745.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.129556 restraints weight = 32343.275| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25932 Z= 0.098 Angle : 0.543 13.327 35301 Z= 0.272 Chirality : 0.043 0.189 3977 Planarity : 0.003 0.048 4569 Dihedral : 4.057 24.933 3457 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 1.87 % Allowed : 16.82 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3190 helix: 1.28 (0.20), residues: 717 sheet: 0.02 (0.20), residues: 666 loop : -1.36 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 317 TYR 0.014 0.001 TYR B1065 PHE 0.036 0.001 PHE C 815 TRP 0.027 0.001 TRP B 104 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00217 (25896) covalent geometry : angle 0.54191 (35229) SS BOND : bond 0.00313 ( 36) SS BOND : angle 0.83884 ( 72) hydrogen bonds : bond 0.03912 ( 912) hydrogen bonds : angle 4.91336 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.63 seconds wall clock time: 57 minutes 12.45 seconds (3432.45 seconds total)