Starting phenix.real_space_refine on Sun Jul 5 05:41:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bno_12231/07_2026/7bno_12231.map" } resolution = 4.2 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= 0.004 sd= 0.042 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 114 5.16 5 C 16227 2.51 5 N 4214 2.21 5 O 4925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25480 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8341 Classifications: {'peptide': 1066} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8336 Classifications: {'peptide': 1065} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1011} Chain breaks: 5 Chain: "C" Number of atoms: 8341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8341 Classifications: {'peptide': 1066} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.41, per 1000 atoms: 0.21 Number of scatterers: 25480 At special positions: 0 Unit cell: (158.95, 153, 198.05, 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 114 16.00 O 4925 8.00 N 4214 7.00 C 16227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 165 " " NAG A1203 " - " ASN A 234 " " NAG A1204 " - " ASN A 282 " " NAG A1205 " - " ASN A 331 " " NAG A1206 " - " ASN A 603 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 709 " " NAG A1209 " - " ASN A 801 " " NAG A1210 " - " ASN A1074 " " NAG A1211 " - " ASN A1134 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 165 " " NAG B1203 " - " ASN B 282 " " NAG B1204 " - " ASN B 603 " " NAG B1205 " - " ASN B 616 " " NAG B1206 " - " ASN B 709 " " NAG B1207 " - " ASN B 717 " " NAG B1208 " - " ASN B 801 " " NAG B1209 " - " ASN B1074 " " NAG B1210 " - " ASN B1134 " " NAG C1201 " - " ASN C 17 " " NAG C1202 " - " ASN C 61 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 616 " " NAG C1207 " - " ASN C 709 " " NAG C1208 " - " ASN C 717 " " NAG C1209 " - " ASN C 801 " " NAG C1210 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5980 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 52 sheets defined 20.8% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.549A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.545A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.591A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.527A pdb=" N PHE A 855 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 852 through 856' Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.745A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.652A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.506A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 965 removed outlier: 3.843A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.711A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.795A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 757 through 782 removed outlier: 4.180A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.706A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B 931 " --> pdb=" O PHE B 927 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 966 removed outlier: 4.135A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.901A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.429A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.523A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.548A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 369' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.597A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.634A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.512A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.712A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.838A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 965 removed outlier: 3.510A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.575A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.079A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.079A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.621A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.793A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.652A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.583A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 154 through 157 removed outlier: 6.277A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.792A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.741A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.279A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 423 through 424 removed outlier: 4.381A pdb=" N GLU A 465 " --> pdb=" O LYS A 424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 553 through 554 removed outlier: 7.164A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.224A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.185A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.500A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.564A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.564A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 861 " --> pdb=" O LYS A 733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.418A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 4.168A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.906A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.599A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 310 through 317 removed outlier: 5.779A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.229A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.921A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.839A pdb=" N ILE C 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.359A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.571A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.883A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.992A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.702A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.129A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.593A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.850A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL C 395 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER C 514 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA C 397 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 512 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER C 399 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 510 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL C 401 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 508 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.522A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.510A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.510A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.072A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.716A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2385 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: 8.20 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7977 1.34 - 1.46: 6300 1.46 - 1.58: 11641 1.58 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 26062 Sorted by residual: bond pdb=" N VAL B 510 " pdb=" CA VAL B 510 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.10e-02 8.26e+03 1.12e+01 bond pdb=" N SER A 98 " pdb=" CA SER A 98 " ideal model delta sigma weight residual 1.459 1.489 -0.030 9.10e-03 1.21e+04 1.07e+01 bond pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.24e-02 6.50e+03 1.05e+01 bond pdb=" N GLY B 431 " pdb=" CA GLY B 431 " ideal model delta sigma weight residual 1.445 1.475 -0.030 9.20e-03 1.18e+04 1.05e+01 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.05e+01 ... (remaining 26057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 33693 2.22 - 4.44: 1619 4.44 - 6.66: 122 6.66 - 8.88: 23 8.88 - 11.10: 5 Bond angle restraints: 35462 Sorted by residual: angle pdb=" N LYS C 41 " pdb=" CA LYS C 41 " pdb=" C LYS C 41 " ideal model delta sigma weight residual 113.02 106.66 6.36 1.20e+00 6.94e-01 2.81e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.85 -6.15 1.22e+00 6.72e-01 2.54e+01 angle pdb=" N GLN B 23 " pdb=" CA GLN B 23 " pdb=" C GLN B 23 " ideal model delta sigma weight residual 108.55 115.83 -7.28 1.62e+00 3.81e-01 2.02e+01 angle pdb=" N MET B 697 " pdb=" CA MET B 697 " pdb=" C MET B 697 " ideal model delta sigma weight residual 110.23 116.48 -6.25 1.45e+00 4.76e-01 1.86e+01 angle pdb=" CA PRO A 986 " pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 117.93 122.92 -4.99 1.20e+00 6.94e-01 1.73e+01 ... (remaining 35457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14140 17.99 - 35.99: 851 35.99 - 53.98: 155 53.98 - 71.98: 65 71.98 - 89.97: 59 Dihedral angle restraints: 15270 sinusoidal: 5970 harmonic: 9300 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 139.71 -46.71 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" C TYR B 265 " pdb=" N TYR B 265 " pdb=" CA TYR B 265 " pdb=" CB TYR B 265 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C TYR B 365 " pdb=" N TYR B 365 " pdb=" CA TYR B 365 " pdb=" CB TYR B 365 " ideal model delta harmonic sigma weight residual -122.60 -131.90 9.30 0 2.50e+00 1.60e-01 1.38e+01 ... (remaining 15267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3669 0.095 - 0.189: 391 0.189 - 0.284: 35 0.284 - 0.379: 3 0.379 - 0.473: 2 Chirality restraints: 4100 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 6.35e+00 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" C1 NAG A1201 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1201 " pdb=" O5 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 4097 not shown) Planarity restraints: 4594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1202 " -0.346 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A1202 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG A1202 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG A1202 " 0.519 2.00e-02 2.50e+03 pdb=" O7 NAG A1202 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1204 " 0.336 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG A1204 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A1204 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG A1204 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG A1204 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1204 " -0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG C1204 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1204 " -0.111 2.00e-02 2.50e+03 pdb=" N2 NAG C1204 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG C1204 " -0.144 2.00e-02 2.50e+03 ... (remaining 4591 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3890 2.75 - 3.29: 24568 3.29 - 3.83: 41993 3.83 - 4.36: 48358 4.36 - 4.90: 82008 Nonbonded interactions: 200817 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR A 22 " pdb=" O THR A 76 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.239 3.040 nonbonded pdb=" NE ARG B1039 " pdb=" OE2 GLU C1031 " model vdw 2.254 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.256 3.120 ... (remaining 200812 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 827 or resid 853 through 1210)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 827 or resid 853 through 1210)) } 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=0.00 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: 13.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.330 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.007 0.117 26137 Z= 0.383 Angle : 1.012 11.100 35645 Z= 0.593 Chirality : 0.059 0.473 4100 Planarity : 0.016 0.295 4562 Dihedral : 14.139 89.973 9164 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.72 % Allowed : 2.79 % Favored : 96.49 % 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: -3.77 (0.12), residues: 3161 helix: -3.47 (0.11), residues: 580 sheet: -1.23 (0.18), residues: 702 loop : -2.80 (0.11), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.073 0.011 ARG B 905 TYR 0.047 0.007 TYR C 473 PHE 0.041 0.003 PHE A 906 TRP 0.031 0.003 TRP B 152 HIS 0.011 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.38 (26062) covalent geometry : angle 1.00442 / 0.59 (35462) SS BOND : bond 0.00494 / 0.34 ( 42) SS BOND : angle 1.53922 / 1.08 ( 84) hydrogen bonds : bond 0.23369 / 15.59 ( 806) hydrogen bonds : angle 8.62126 / 5.92 ( 2385) link_BETA1-4 : bond 0.00449 / 0.24 ( 1) link_BETA1-4 : angle 1.17473 / 0.63 ( 3) link_NAG-ASN : bond 0.00679 / 0.49 ( 32) link_NAG-ASN : angle 2.32395 / 1.57 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.5502 (p0) cc_final: 0.5216 (p0) REVERT: A 731 MET cc_start: 0.8891 (ppp) cc_final: 0.7947 (ppp) REVERT: B 79 PHE cc_start: 0.9091 (t80) cc_final: 0.8800 (t80) REVERT: B 869 MET cc_start: 0.9124 (mtt) cc_final: 0.8820 (ptp) REVERT: C 96 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.5772 (tp30) REVERT: C 118 LEU cc_start: 0.8921 (mp) cc_final: 0.8674 (mt) REVERT: C 329 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8905 (t80) REVERT: C 564 GLN cc_start: 0.9034 (mt0) cc_final: 0.8730 (pm20) REVERT: C 901 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7854 (tm-30) outliers start: 20 outliers final: 5 residues processed: 161 average time/residue: 0.1826 time to fit residues: 46.9520 Evaluate side-chains 97 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 115 GLN A 164 ASN A 394 ASN A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN A1101 HIS B 164 ASN B 183 GLN B 207 HIS B 506 GLN B 703 ASN B 804 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 450 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 957 GLN C1071 GLN C1101 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.060823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040364 restraints weight = 169314.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.041851 restraints weight = 90204.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.042836 restraints weight = 59844.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.043500 restraints weight = 45453.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.043912 restraints weight = 37633.559| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 26137 Z= 0.260 Angle : 0.750 14.716 35645 Z= 0.388 Chirality : 0.047 0.273 4100 Planarity : 0.005 0.057 4562 Dihedral : 4.717 44.551 3431 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.11 % Allowed : 2.90 % Favored : 96.99 % 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: -2.07 (0.13), residues: 3161 helix: -0.12 (0.20), residues: 594 sheet: -0.79 (0.18), residues: 729 loop : -2.14 (0.12), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.019 0.002 TYR C 904 PHE 0.021 0.002 PHE A1042 TRP 0.022 0.002 TRP A 64 HIS 0.008 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.26 (26062) covalent geometry : angle 0.74121 / 0.39 (35462) SS BOND : bond 0.00371 / 0.23 ( 42) SS BOND : angle 1.11032 / 0.80 ( 84) hydrogen bonds : bond 0.06142 / 4.05 ( 806) hydrogen bonds : angle 6.41341 / 4.38 ( 2385) link_BETA1-4 : bond 0.00718 / 0.38 ( 1) link_BETA1-4 : angle 1.47029 / 0.82 ( 3) link_NAG-ASN : bond 0.00339 / 0.21 ( 32) link_NAG-ASN : angle 2.12286 / 1.40 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9001 (ppp) cc_final: 0.7994 (ppp) REVERT: A 869 MET cc_start: 0.9055 (ptm) cc_final: 0.8809 (ptm) REVERT: B 177 MET cc_start: 0.3576 (ptt) cc_final: 0.3230 (ptp) REVERT: B 331 ASN cc_start: 0.8232 (t0) cc_final: 0.7996 (t0) REVERT: C 118 LEU cc_start: 0.8921 (mp) cc_final: 0.8697 (mp) REVERT: C 775 ASP cc_start: 0.8878 (p0) cc_final: 0.8563 (p0) REVERT: C 777 ASN cc_start: 0.9221 (m-40) cc_final: 0.8615 (m110) outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.1740 time to fit residues: 31.4792 Evaluate side-chains 78 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 11 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1088 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.060986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.040456 restraints weight = 167318.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041973 restraints weight = 89223.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.042989 restraints weight = 59158.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043683 restraints weight = 44440.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.044107 restraints weight = 36787.608| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26137 Z= 0.163 Angle : 0.597 12.087 35645 Z= 0.309 Chirality : 0.044 0.272 4100 Planarity : 0.004 0.062 4562 Dihedral : 4.396 41.595 3431 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.74 % 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: -1.40 (0.14), residues: 3161 helix: 0.99 (0.21), residues: 606 sheet: -0.62 (0.19), residues: 724 loop : -1.80 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1000 TYR 0.019 0.001 TYR A 917 PHE 0.028 0.001 PHE B 490 TRP 0.014 0.001 TRP C 152 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (26062) covalent geometry : angle 0.59003 / 0.31 (35462) SS BOND : bond 0.00244 / 0.15 ( 42) SS BOND : angle 0.78797 / 0.56 ( 84) hydrogen bonds : bond 0.05049 / 3.34 ( 806) hydrogen bonds : angle 5.72791 / 3.90 ( 2385) link_BETA1-4 : bond 0.00505 / 0.27 ( 1) link_BETA1-4 : angle 1.30642 / 0.73 ( 3) link_NAG-ASN : bond 0.00269 / 0.19 ( 32) link_NAG-ASN : angle 1.71497 / 1.13 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8724 (tp) cc_final: 0.8520 (tp) REVERT: A 731 MET cc_start: 0.9033 (ppp) cc_final: 0.7941 (ppp) REVERT: A 1002 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8417 (tm-30) REVERT: B 177 MET cc_start: 0.3604 (ptt) cc_final: 0.3337 (ptp) REVERT: B 331 ASN cc_start: 0.8226 (t0) cc_final: 0.7991 (t0) REVERT: B 697 MET cc_start: 0.8437 (ptm) cc_final: 0.7908 (ttp) REVERT: C 118 LEU cc_start: 0.8894 (mp) cc_final: 0.8691 (mp) REVERT: C 775 ASP cc_start: 0.8734 (p0) cc_final: 0.8443 (p0) REVERT: C 777 ASN cc_start: 0.9045 (m-40) cc_final: 0.8526 (m110) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1677 time to fit residues: 30.1199 Evaluate side-chains 76 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 184 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 291 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 308 optimal weight: 0.6980 chunk 222 optimal weight: 10.0000 chunk 214 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 164 ASN B 703 ASN B 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 895 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.061519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.041017 restraints weight = 166263.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.042568 restraints weight = 87824.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043584 restraints weight = 57864.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.044258 restraints weight = 43757.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.044709 restraints weight = 36239.860| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 26137 Z= 0.112 Angle : 0.540 10.156 35645 Z= 0.276 Chirality : 0.044 0.245 4100 Planarity : 0.004 0.063 4562 Dihedral : 4.155 37.304 3431 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.57 % 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: -1.06 (0.14), residues: 3161 helix: 1.42 (0.21), residues: 604 sheet: -0.37 (0.19), residues: 718 loop : -1.66 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.015 0.001 TYR A 741 PHE 0.014 0.001 PHE B 490 TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (26062) covalent geometry : angle 0.53347 / 0.27 (35462) SS BOND : bond 0.00203 / 0.12 ( 42) SS BOND : angle 1.03441 / 0.65 ( 84) hydrogen bonds : bond 0.04403 / 2.91 ( 806) hydrogen bonds : angle 5.27606 / 3.60 ( 2385) link_BETA1-4 : bond 0.00161 / 0.08 ( 1) link_BETA1-4 : angle 1.08546 / 0.60 ( 3) link_NAG-ASN : bond 0.00269 / 0.21 ( 32) link_NAG-ASN : angle 1.50494 / 1.01 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9420 (p) cc_final: 0.9204 (m) REVERT: A 731 MET cc_start: 0.8994 (ppp) cc_final: 0.8066 (ppp) REVERT: A 1002 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8337 (tm-30) REVERT: B 177 MET cc_start: 0.3595 (ptt) cc_final: 0.3367 (ptp) REVERT: B 331 ASN cc_start: 0.8294 (t0) cc_final: 0.8091 (t0) REVERT: B 697 MET cc_start: 0.8423 (ptm) cc_final: 0.7979 (ttp) REVERT: C 118 LEU cc_start: 0.8893 (mp) cc_final: 0.8675 (mp) REVERT: C 276 LEU cc_start: 0.9483 (tp) cc_final: 0.9240 (tp) REVERT: C 775 ASP cc_start: 0.8684 (p0) cc_final: 0.8373 (p0) REVERT: C 777 ASN cc_start: 0.8983 (m-40) cc_final: 0.8172 (m110) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1597 time to fit residues: 29.2535 Evaluate side-chains 77 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 140 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 310 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 268 optimal weight: 0.6980 chunk 300 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 188 ASN A 804 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1113 GLN B 196 ASN B 703 ASN B 751 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C1101 HIS C1142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.059621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039623 restraints weight = 171062.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.041504 restraints weight = 100649.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.041908 restraints weight = 57861.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.042304 restraints weight = 45235.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.042529 restraints weight = 41077.859| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 26137 Z= 0.274 Angle : 0.675 10.770 35645 Z= 0.345 Chirality : 0.045 0.245 4100 Planarity : 0.004 0.064 4562 Dihedral : 4.425 31.425 3431 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % 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: -1.19 (0.14), residues: 3161 helix: 1.02 (0.21), residues: 609 sheet: -0.51 (0.19), residues: 738 loop : -1.60 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.014 0.002 TYR B 904 PHE 0.019 0.002 PHE A 906 TRP 0.012 0.002 TRP C 64 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 (26062) covalent geometry : angle 0.66711 / 0.34 (35462) SS BOND : bond 0.00324 / 0.21 ( 42) SS BOND : angle 1.19893 / 0.78 ( 84) hydrogen bonds : bond 0.04989 / 3.27 ( 806) hydrogen bonds : angle 5.62590 / 3.83 ( 2385) link_BETA1-4 : bond 0.00061 / 0.03 ( 1) link_BETA1-4 : angle 1.28996 / 0.72 ( 3) link_NAG-ASN : bond 0.00344 / 0.21 ( 32) link_NAG-ASN : angle 1.90391 / 1.22 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8726 (tpp) cc_final: 0.8341 (tpt) REVERT: A 731 MET cc_start: 0.8557 (ppp) cc_final: 0.7859 (ppp) REVERT: A 1002 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8573 (tm-30) REVERT: B 177 MET cc_start: 0.4139 (ptt) cc_final: 0.3692 (ptp) REVERT: B 331 ASN cc_start: 0.8513 (t0) cc_final: 0.8291 (t0) REVERT: B 697 MET cc_start: 0.8463 (ptm) cc_final: 0.8010 (ttp) REVERT: C 118 LEU cc_start: 0.8941 (mp) cc_final: 0.8735 (mp) REVERT: C 276 LEU cc_start: 0.9576 (tp) cc_final: 0.9341 (tp) REVERT: C 775 ASP cc_start: 0.8784 (p0) cc_final: 0.8521 (p0) REVERT: C 777 ASN cc_start: 0.8739 (m-40) cc_final: 0.8208 (m110) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1465 time to fit residues: 24.0569 Evaluate side-chains 66 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 125 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 195 optimal weight: 0.0770 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 294 optimal weight: 0.6980 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1011 GLN B 703 ASN B 779 GLN B 935 GLN C 487 ASN C1083 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.059700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.040016 restraints weight = 168840.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.041824 restraints weight = 91852.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.042564 restraints weight = 50715.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042808 restraints weight = 40631.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.042857 restraints weight = 36587.129| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26137 Z= 0.173 Angle : 0.572 9.376 35645 Z= 0.294 Chirality : 0.043 0.204 4100 Planarity : 0.004 0.061 4562 Dihedral : 4.302 25.952 3431 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 0.04 % Allowed : 1.40 % Favored : 98.57 % 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: -1.03 (0.14), residues: 3161 helix: 1.19 (0.21), residues: 611 sheet: -0.35 (0.19), residues: 707 loop : -1.54 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.012 0.001 TYR A1067 PHE 0.031 0.001 PHE C 486 TRP 0.013 0.001 TRP C 152 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (26062) covalent geometry : angle 0.56564 / 0.29 (35462) SS BOND : bond 0.00329 / 0.19 ( 42) SS BOND : angle 0.97726 / 0.63 ( 84) hydrogen bonds : bond 0.04541 / 2.99 ( 806) hydrogen bonds : angle 5.35869 / 3.65 ( 2385) link_BETA1-4 : bond 0.00113 / 0.06 ( 1) link_BETA1-4 : angle 1.06480 / 0.60 ( 3) link_NAG-ASN : bond 0.00223 / 0.14 ( 32) link_NAG-ASN : angle 1.54103 / 1.01 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.9541 (m-40) cc_final: 0.8842 (p0) REVERT: A 697 MET cc_start: 0.8718 (tpp) cc_final: 0.8469 (tpt) REVERT: A 731 MET cc_start: 0.8573 (ppp) cc_final: 0.7780 (ppp) REVERT: A 1002 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8654 (tm-30) REVERT: B 177 MET cc_start: 0.4229 (ptt) cc_final: 0.3802 (ptp) REVERT: B 331 ASN cc_start: 0.8493 (t0) cc_final: 0.8248 (t0) REVERT: B 697 MET cc_start: 0.8455 (ptm) cc_final: 0.7989 (ttp) REVERT: C 118 LEU cc_start: 0.8935 (mp) cc_final: 0.8733 (mp) REVERT: C 275 PHE cc_start: 0.8865 (m-80) cc_final: 0.8536 (m-10) REVERT: C 754 LEU cc_start: 0.9680 (tt) cc_final: 0.9413 (mp) REVERT: C 775 ASP cc_start: 0.8741 (p0) cc_final: 0.8502 (p0) REVERT: C 777 ASN cc_start: 0.8683 (m-40) cc_final: 0.8216 (m110) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1658 time to fit residues: 25.1279 Evaluate side-chains 65 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 132 optimal weight: 6.9990 chunk 168 optimal weight: 0.0570 chunk 58 optimal weight: 0.9990 chunk 212 optimal weight: 30.0000 chunk 230 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 703 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.059643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.039517 restraints weight = 167133.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.041536 restraints weight = 91572.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.042331 restraints weight = 50755.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.042701 restraints weight = 37676.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.042856 restraints weight = 34325.574| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26137 Z= 0.168 Angle : 0.564 9.465 35645 Z= 0.289 Chirality : 0.043 0.199 4100 Planarity : 0.004 0.062 4562 Dihedral : 4.248 21.729 3431 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.85 % 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: -0.98 (0.14), residues: 3161 helix: 1.22 (0.21), residues: 612 sheet: -0.30 (0.19), residues: 720 loop : -1.52 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.013 0.001 TYR A 917 PHE 0.021 0.001 PHE C 486 TRP 0.012 0.001 TRP C 152 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (26062) covalent geometry : angle 0.55786 / 0.29 (35462) SS BOND : bond 0.00320 / 0.20 ( 42) SS BOND : angle 0.96877 / 0.61 ( 84) hydrogen bonds : bond 0.04494 / 2.96 ( 806) hydrogen bonds : angle 5.29727 / 3.61 ( 2385) link_BETA1-4 : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : angle 1.09060 / 0.61 ( 3) link_NAG-ASN : bond 0.00171 / 0.11 ( 32) link_NAG-ASN : angle 1.45075 / 0.96 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.9526 (m-40) cc_final: 0.8818 (p0) REVERT: A 731 MET cc_start: 0.8612 (ppp) cc_final: 0.7824 (ppp) REVERT: A 1002 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8628 (tm-30) REVERT: B 177 MET cc_start: 0.4313 (ptt) cc_final: 0.3898 (ptp) REVERT: B 331 ASN cc_start: 0.8468 (t0) cc_final: 0.8231 (t0) REVERT: B 697 MET cc_start: 0.8438 (ptm) cc_final: 0.7973 (ttp) REVERT: C 223 LEU cc_start: 0.9297 (mp) cc_final: 0.8282 (mp) REVERT: C 275 PHE cc_start: 0.8857 (m-80) cc_final: 0.8533 (m-10) REVERT: C 754 LEU cc_start: 0.9681 (tt) cc_final: 0.9431 (mp) REVERT: C 775 ASP cc_start: 0.8742 (p0) cc_final: 0.8497 (p0) REVERT: C 777 ASN cc_start: 0.8680 (m-40) cc_final: 0.8229 (m110) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1571 time to fit residues: 26.0694 Evaluate side-chains 68 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 167 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 263 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN B 146 HIS B 703 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.059642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.039162 restraints weight = 167425.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.040680 restraints weight = 87190.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.041686 restraints weight = 57047.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.042359 restraints weight = 42920.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.042769 restraints weight = 35431.465| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26137 Z= 0.151 Angle : 0.543 9.865 35645 Z= 0.279 Chirality : 0.043 0.362 4100 Planarity : 0.004 0.061 4562 Dihedral : 4.179 20.718 3431 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.04 % Allowed : 0.64 % Favored : 99.32 % 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: -0.90 (0.14), residues: 3161 helix: 1.36 (0.21), residues: 612 sheet: -0.26 (0.19), residues: 725 loop : -1.49 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.012 0.001 TYR A1067 PHE 0.017 0.001 PHE C 486 TRP 0.012 0.001 TRP C 152 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (26062) covalent geometry : angle 0.53797 / 0.28 (35462) SS BOND : bond 0.00232 / 0.14 ( 42) SS BOND : angle 0.95301 / 0.65 ( 84) hydrogen bonds : bond 0.04320 / 2.86 ( 806) hydrogen bonds : angle 5.13452 / 3.49 ( 2385) link_BETA1-4 : bond 0.00026 / 0.01 ( 1) link_BETA1-4 : angle 1.12656 / 0.62 ( 3) link_NAG-ASN : bond 0.00155 / 0.10 ( 32) link_NAG-ASN : angle 1.37309 / 0.95 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8605 (ppp) cc_final: 0.7807 (ppp) REVERT: A 773 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8787 (mt-10) REVERT: A 1002 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8591 (tm-30) REVERT: B 177 MET cc_start: 0.4210 (ptt) cc_final: 0.3779 (ptp) REVERT: B 697 MET cc_start: 0.8452 (ptm) cc_final: 0.8030 (ttp) REVERT: C 275 PHE cc_start: 0.8856 (m-80) cc_final: 0.8512 (m-10) REVERT: C 775 ASP cc_start: 0.8750 (p0) cc_final: 0.8506 (p0) REVERT: C 777 ASN cc_start: 0.8685 (m-40) cc_final: 0.8227 (m110) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1595 time to fit residues: 26.9319 Evaluate side-chains 73 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 102 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 955 ASN B 448 ASN B 703 ASN B 954 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.039378 restraints weight = 167838.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041270 restraints weight = 91720.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.042231 restraints weight = 51254.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.042490 restraints weight = 37747.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.042624 restraints weight = 34137.994| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26137 Z= 0.173 Angle : 0.572 10.249 35645 Z= 0.291 Chirality : 0.044 0.353 4100 Planarity : 0.004 0.062 4562 Dihedral : 4.203 20.875 3431 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.53 % 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: -0.92 (0.14), residues: 3161 helix: 1.25 (0.21), residues: 612 sheet: -0.20 (0.19), residues: 724 loop : -1.50 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1107 TYR 0.015 0.001 TYR A 917 PHE 0.021 0.001 PHE C 106 TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (26062) covalent geometry : angle 0.56352 / 0.29 (35462) SS BOND : bond 0.00244 / 0.15 ( 42) SS BOND : angle 0.99145 / 0.65 ( 84) hydrogen bonds : bond 0.04446 / 2.93 ( 806) hydrogen bonds : angle 5.22982 / 3.56 ( 2385) link_BETA1-4 : bond 0.00120 / 0.06 ( 1) link_BETA1-4 : angle 1.19046 / 0.66 ( 3) link_NAG-ASN : bond 0.00179 / 0.12 ( 32) link_NAG-ASN : angle 1.80712 / 1.11 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8589 (tp) cc_final: 0.8388 (tp) REVERT: A 731 MET cc_start: 0.8581 (ppp) cc_final: 0.7784 (ppp) REVERT: A 1002 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 1019 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8352 (tpp80) REVERT: B 177 MET cc_start: 0.4394 (ptt) cc_final: 0.4000 (ptp) REVERT: B 697 MET cc_start: 0.8456 (ptm) cc_final: 0.8025 (ttp) REVERT: C 216 LEU cc_start: 0.8687 (tp) cc_final: 0.8474 (tp) REVERT: C 775 ASP cc_start: 0.8751 (p0) cc_final: 0.8524 (p0) REVERT: C 777 ASN cc_start: 0.8688 (m-40) cc_final: 0.8203 (m110) REVERT: C 957 GLN cc_start: 0.9337 (mp10) cc_final: 0.9108 (mp10) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1637 time to fit residues: 25.2455 Evaluate side-chains 69 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 139 optimal weight: 0.0980 chunk 272 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 703 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.059663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.039722 restraints weight = 167698.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.041609 restraints weight = 91685.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.042588 restraints weight = 50042.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042875 restraints weight = 36448.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.042995 restraints weight = 33510.635| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26137 Z= 0.138 Angle : 0.543 10.302 35645 Z= 0.277 Chirality : 0.043 0.300 4100 Planarity : 0.004 0.061 4562 Dihedral : 4.139 20.436 3431 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 0.04 % Allowed : 0.14 % Favored : 99.82 % 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: -0.83 (0.15), residues: 3161 helix: 1.39 (0.21), residues: 612 sheet: -0.17 (0.19), residues: 719 loop : -1.44 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.014 0.001 TYR B 756 PHE 0.017 0.001 PHE A 906 TRP 0.011 0.001 TRP C 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (26062) covalent geometry : angle 0.53273 / 0.27 (35462) SS BOND : bond 0.00213 / 0.13 ( 42) SS BOND : angle 0.89398 / 0.60 ( 84) hydrogen bonds : bond 0.04266 / 2.82 ( 806) hydrogen bonds : angle 5.09388 / 3.46 ( 2385) link_BETA1-4 : bond 0.00327 / 0.17 ( 1) link_BETA1-4 : angle 1.20677 / 0.66 ( 3) link_NAG-ASN : bond 0.00154 / 0.11 ( 32) link_NAG-ASN : angle 1.94319 / 1.24 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.9503 (m-40) cc_final: 0.8697 (p0) REVERT: A 731 MET cc_start: 0.8610 (ppp) cc_final: 0.7809 (ppp) REVERT: A 1002 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8577 (tm-30) REVERT: B 177 MET cc_start: 0.4497 (ptt) cc_final: 0.4124 (ptp) REVERT: B 697 MET cc_start: 0.8459 (ptm) cc_final: 0.8041 (ttp) REVERT: C 216 LEU cc_start: 0.8659 (tp) cc_final: 0.8453 (tp) REVERT: C 775 ASP cc_start: 0.8707 (p0) cc_final: 0.8457 (p0) REVERT: C 777 ASN cc_start: 0.8679 (m-40) cc_final: 0.8209 (m110) REVERT: C 957 GLN cc_start: 0.9341 (mp10) cc_final: 0.9100 (mp10) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1656 time to fit residues: 26.8614 Evaluate side-chains 69 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 198 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 42 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 266 optimal weight: 0.0570 chunk 175 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 195 optimal weight: 0.0050 chunk 12 optimal weight: 7.9990 overall best weight: 0.8274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 703 ASN B 751 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.060284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.040053 restraints weight = 166423.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.041597 restraints weight = 86293.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.042611 restraints weight = 56535.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043311 restraints weight = 42346.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.043762 restraints weight = 34872.220| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26137 Z= 0.101 Angle : 0.514 10.907 35645 Z= 0.261 Chirality : 0.043 0.285 4100 Planarity : 0.004 0.061 4562 Dihedral : 3.930 19.494 3431 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 0.04 % Allowed : 0.14 % Favored : 99.82 % 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: -0.67 (0.15), residues: 3161 helix: 1.61 (0.22), residues: 613 sheet: -0.07 (0.19), residues: 709 loop : -1.37 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1000 TYR 0.011 0.001 TYR A1067 PHE 0.022 0.001 PHE A 970 TRP 0.012 0.001 TRP C 152 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (26062) covalent geometry : angle 0.50783 / 0.26 (35462) SS BOND : bond 0.00168 / 0.10 ( 42) SS BOND : angle 0.80834 / 0.55 ( 84) hydrogen bonds : bond 0.03911 / 2.60 ( 806) hydrogen bonds : angle 4.86183 / 3.30 ( 2385) link_BETA1-4 : bond 0.00264 / 0.14 ( 1) link_BETA1-4 : angle 1.22516 / 0.66 ( 3) link_NAG-ASN : bond 0.00182 / 0.13 ( 32) link_NAG-ASN : angle 1.52114 / 0.97 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4584.81 seconds wall clock time: 80 minutes 42.22 seconds (4842.22 seconds total)