Starting phenix.real_space_refine on Thu Mar 5 22:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bno_12231/03_2026/7bno_12231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bno_12231/03_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_12231/03_2026/7bno_12231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bno_12231/03_2026/7bno_12231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bno_12231/03_2026/7bno_12231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bno_12231/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 33 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.00, per 1000 atoms: 0.24 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 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: 1.30 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: 5.65 Time building geometry restraints manager: 2.88 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: 14797 17.99 - 35.99: 884 35.99 - 53.98: 158 53.98 - 71.98: 65 71.98 - 89.97: 59 Dihedral angle restraints: 15963 sinusoidal: 6663 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 15960 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: 9.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.820 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 13.777 89.973 9857 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 covalent geometry : bond 0.00715 (26062) covalent geometry : angle 1.00442 (35462) SS BOND : bond 0.00494 ( 42) SS BOND : angle 1.53922 ( 84) hydrogen bonds : bond 0.23369 ( 806) hydrogen bonds : angle 8.62126 ( 2385) link_BETA1-4 : bond 0.00449 ( 1) link_BETA1-4 : angle 1.17473 ( 3) link_NAG-ASN : bond 0.00679 ( 32) link_NAG-ASN : angle 2.32395 ( 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 : 1.043 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: 0.1885 time to fit residues: 47.8706 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 : 0.839 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 52 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 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 Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.060878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.040423 restraints weight = 169312.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.041921 restraints weight = 90458.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.042911 restraints weight = 59748.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043549 restraints weight = 45324.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.044003 restraints weight = 37708.820| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 26137 Z= 0.260 Angle : 0.743 14.749 35645 Z= 0.386 Chirality : 0.046 0.304 4100 Planarity : 0.005 0.058 4562 Dihedral : 5.684 57.778 4124 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.92 % 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: -0.09 (0.20), residues: 595 sheet: -0.76 (0.19), residues: 723 loop : -2.16 (0.12), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.018 0.002 TYR B 380 PHE 0.021 0.002 PHE A1042 TRP 0.022 0.002 TRP A 64 HIS 0.011 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00563 (26062) covalent geometry : angle 0.73432 (35462) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.08631 ( 84) hydrogen bonds : bond 0.06028 ( 806) hydrogen bonds : angle 6.44153 ( 2385) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 1.95020 ( 3) link_NAG-ASN : bond 0.00487 ( 32) link_NAG-ASN : angle 2.12872 ( 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 : 1.059 Fit side-chains 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: 0.7990 (ppp) REVERT: A 869 MET cc_start: 0.9083 (ptm) cc_final: 0.8834 (ptm) REVERT: B 177 MET cc_start: 0.3620 (ptt) cc_final: 0.3278 (ptp) REVERT: B 331 ASN cc_start: 0.8266 (t0) cc_final: 0.8035 (t0) REVERT: C 118 LEU cc_start: 0.8928 (mp) cc_final: 0.8700 (mp) REVERT: C 775 ASP cc_start: 0.8890 (p0) cc_final: 0.8587 (p0) REVERT: C 777 ASN cc_start: 0.9206 (m-40) cc_final: 0.8602 (m110) outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.1717 time to fit residues: 31.0810 Evaluate side-chains 77 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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: 2.9990 chunk 57 optimal weight: 0.9990 chunk 289 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 251 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** 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 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 = 0.3527 r_free = 0.3527 target = 0.061001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040515 restraints weight = 168610.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.042002 restraints weight = 90829.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.043002 restraints weight = 60594.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043671 restraints weight = 45907.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.044111 restraints weight = 38083.984| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26137 Z= 0.168 Angle : 0.599 12.044 35645 Z= 0.310 Chirality : 0.044 0.283 4100 Planarity : 0.004 0.061 4562 Dihedral : 5.024 53.304 4124 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.82 % 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: -1.39 (0.14), residues: 3161 helix: 0.99 (0.21), residues: 605 sheet: -0.61 (0.19), residues: 731 loop : -1.80 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1000 TYR 0.014 0.001 TYR C 904 PHE 0.027 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 covalent geometry : bond 0.00367 (26062) covalent geometry : angle 0.59191 (35462) SS BOND : bond 0.00226 ( 42) SS BOND : angle 0.90943 ( 84) hydrogen bonds : bond 0.05036 ( 806) hydrogen bonds : angle 5.71913 ( 2385) link_BETA1-4 : bond 0.00080 ( 1) link_BETA1-4 : angle 1.15738 ( 3) link_NAG-ASN : bond 0.00269 ( 32) link_NAG-ASN : angle 1.79810 ( 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 108 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8726 (tp) cc_final: 0.8524 (tp) REVERT: A 731 MET cc_start: 0.9024 (ppp) cc_final: 0.7939 (ppp) REVERT: A 1002 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 177 MET cc_start: 0.3587 (ptt) cc_final: 0.3317 (ptp) REVERT: B 331 ASN cc_start: 0.8251 (t0) cc_final: 0.7999 (t0) REVERT: B 697 MET cc_start: 0.8459 (ptm) cc_final: 0.7931 (ttp) REVERT: C 118 LEU cc_start: 0.8884 (mp) cc_final: 0.8683 (mp) REVERT: C 775 ASP cc_start: 0.8741 (p0) cc_final: 0.8455 (p0) REVERT: C 777 ASN cc_start: 0.9037 (m-40) cc_final: 0.8508 (m110) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1649 time to fit residues: 29.8158 Evaluate side-chains 75 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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: 0.8980 chunk 240 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 308 optimal weight: 0.6980 chunk 222 optimal weight: 10.0000 chunk 214 optimal weight: 0.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.061392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040949 restraints weight = 166471.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.042451 restraints weight = 88769.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.043471 restraints weight = 58892.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.044117 restraints weight = 44658.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.044584 restraints weight = 37089.103| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26137 Z= 0.118 Angle : 0.545 11.480 35645 Z= 0.279 Chirality : 0.043 0.255 4100 Planarity : 0.004 0.062 4562 Dihedral : 4.717 55.276 4124 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3161 helix: 1.41 (0.21), residues: 604 sheet: -0.40 (0.19), residues: 724 loop : -1.64 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.015 0.001 TYR A 741 PHE 0.013 0.001 PHE A1062 TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00260 (26062) covalent geometry : angle 0.53671 (35462) SS BOND : bond 0.00451 ( 42) SS BOND : angle 1.10109 ( 84) hydrogen bonds : bond 0.04458 ( 806) hydrogen bonds : angle 5.31719 ( 2385) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 1.11580 ( 3) link_NAG-ASN : bond 0.00258 ( 32) link_NAG-ASN : angle 1.64737 ( 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 : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9418 (p) cc_final: 0.9199 (m) REVERT: A 731 MET cc_start: 0.9009 (ppp) cc_final: 0.8081 (ppp) REVERT: A 1002 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8346 (tm-30) REVERT: B 177 MET cc_start: 0.3614 (ptt) cc_final: 0.3381 (ptp) REVERT: B 331 ASN cc_start: 0.8327 (t0) cc_final: 0.8080 (t0) REVERT: B 697 MET cc_start: 0.8418 (ptm) cc_final: 0.7988 (ttp) REVERT: C 118 LEU cc_start: 0.8893 (mp) cc_final: 0.8679 (mp) REVERT: C 276 LEU cc_start: 0.9497 (tp) cc_final: 0.9247 (tp) REVERT: C 775 ASP cc_start: 0.8693 (p0) cc_final: 0.8369 (p0) REVERT: C 777 ASN cc_start: 0.9002 (m-40) cc_final: 0.8385 (m110) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1554 time to fit residues: 28.2906 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 : 0.813 ------------------------------------------------------------------------------- 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: 1.9990 chunk 170 optimal weight: 8.9990 chunk 289 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 300 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 188 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 196 ASN B 703 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN 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 = 0.059424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.039361 restraints weight = 170868.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.041273 restraints weight = 98273.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.042301 restraints weight = 55346.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042569 restraints weight = 42186.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.042584 restraints weight = 34885.353| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 26137 Z= 0.277 Angle : 0.690 10.891 35645 Z= 0.352 Chirality : 0.045 0.351 4100 Planarity : 0.004 0.065 4562 Dihedral : 5.020 55.461 4124 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -1.24 (0.14), residues: 3161 helix: 0.86 (0.21), residues: 611 sheet: -0.50 (0.19), residues: 733 loop : -1.60 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1019 TYR 0.017 0.002 TYR B 904 PHE 0.021 0.002 PHE A1052 TRP 0.015 0.002 TRP A 64 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00609 (26062) covalent geometry : angle 0.67902 (35462) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.30834 ( 84) hydrogen bonds : bond 0.05125 ( 806) hydrogen bonds : angle 5.68018 ( 2385) link_BETA1-4 : bond 0.00182 ( 1) link_BETA1-4 : angle 1.61661 ( 3) link_NAG-ASN : bond 0.00334 ( 32) link_NAG-ASN : angle 2.15787 ( 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 94 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.006 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: 0.8718 (tpp) cc_final: 0.8324 (tpt) REVERT: A 731 MET cc_start: 0.8531 (ppp) cc_final: 0.7808 (ppp) REVERT: A 1002 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8559 (tm-30) REVERT: B 177 MET cc_start: 0.4130 (ptt) cc_final: 0.3683 (ptp) REVERT: B 331 ASN cc_start: 0.8500 (t0) cc_final: 0.8269 (t0) REVERT: B 697 MET cc_start: 0.8454 (ptm) cc_final: 0.8001 (ttp) REVERT: C 276 LEU cc_start: 0.9588 (tp) cc_final: 0.9340 (tp) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1559 time to fit residues: 24.7066 Evaluate side-chains 64 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 3.9990 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 chunk 195 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 chunk 294 optimal weight: 0.5980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN A1011 GLN B 703 ASN B 779 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.059760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.040131 restraints weight = 170103.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.041631 restraints weight = 91881.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042842 restraints weight = 53556.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042907 restraints weight = 45007.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042922 restraints weight = 37524.180| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26137 Z= 0.164 Angle : 0.565 9.573 35645 Z= 0.291 Chirality : 0.043 0.214 4100 Planarity : 0.004 0.060 4562 Dihedral : 4.825 55.994 4124 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 0.04 % Allowed : 1.22 % Favored : 98.75 % 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: -1.04 (0.14), residues: 3161 helix: 1.21 (0.21), residues: 611 sheet: -0.35 (0.19), residues: 703 loop : -1.55 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.013 0.001 TYR A 741 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 covalent geometry : bond 0.00360 (26062) covalent geometry : angle 0.55667 (35462) SS BOND : bond 0.00240 ( 42) SS BOND : angle 1.02284 ( 84) hydrogen bonds : bond 0.04598 ( 806) hydrogen bonds : angle 5.36237 ( 2385) link_BETA1-4 : bond 0.00187 ( 1) link_BETA1-4 : angle 1.04660 ( 3) link_NAG-ASN : bond 0.00193 ( 32) link_NAG-ASN : angle 1.73505 ( 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 96 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.908 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: 0.9552 (m-40) cc_final: 0.8857 (p0) REVERT: A 697 MET cc_start: 0.8753 (tpp) cc_final: 0.8417 (tpt) REVERT: A 731 MET cc_start: 0.8579 (ppp) cc_final: 0.7802 (ppp) REVERT: A 1002 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8615 (tm-30) REVERT: B 177 MET cc_start: 0.4271 (ptt) cc_final: 0.3839 (ptp) REVERT: B 331 ASN cc_start: 0.8440 (t0) cc_final: 0.8181 (t0) REVERT: B 697 MET cc_start: 0.8445 (ptm) cc_final: 0.7973 (ttp) REVERT: C 275 PHE cc_start: 0.8868 (m-80) cc_final: 0.8479 (m-10) REVERT: C 276 LEU cc_start: 0.9531 (tp) cc_final: 0.9298 (tp) REVERT: C 754 LEU cc_start: 0.9679 (tt) cc_final: 0.9415 (mp) REVERT: C 777 ASN cc_start: 0.9055 (m-40) cc_final: 0.8504 (m110) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1661 time to fit residues: 27.0569 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 : 1.076 ------------------------------------------------------------------------------- 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: 4.9990 chunk 168 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 212 optimal weight: 30.0000 chunk 230 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 ASN B 935 GLN C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.060470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.040015 restraints weight = 168142.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041500 restraints weight = 89652.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042491 restraints weight = 59567.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043144 restraints weight = 45206.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.043583 restraints weight = 37795.314| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3034 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= 0.112 Angle : 0.524 10.158 35645 Z= 0.269 Chirality : 0.043 0.209 4100 Planarity : 0.004 0.061 4562 Dihedral : 4.510 55.338 4124 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 0.04 % Allowed : 0.97 % Favored : 99.00 % 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: -0.89 (0.14), residues: 3161 helix: 1.33 (0.21), residues: 613 sheet: -0.28 (0.19), residues: 724 loop : -1.46 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.011 0.001 TYR A1067 PHE 0.022 0.001 PHE C 486 TRP 0.012 0.001 TRP C 152 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00247 (26062) covalent geometry : angle 0.51759 (35462) SS BOND : bond 0.00240 ( 42) SS BOND : angle 0.82516 ( 84) hydrogen bonds : bond 0.04215 ( 806) hydrogen bonds : angle 5.11717 ( 2385) link_BETA1-4 : bond 0.00466 ( 1) link_BETA1-4 : angle 1.22326 ( 3) link_NAG-ASN : bond 0.00191 ( 32) link_NAG-ASN : angle 1.47857 ( 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 105 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.001 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 90 VAL cc_start: 0.9385 (p) cc_final: 0.9138 (m) REVERT: A 544 ASN cc_start: 0.9426 (m-40) cc_final: 0.8676 (p0) REVERT: A 731 MET cc_start: 0.8510 (ppp) cc_final: 0.7758 (ppp) REVERT: A 1002 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8385 (tm-30) REVERT: B 177 MET cc_start: 0.4023 (ptt) cc_final: 0.3589 (ptp) REVERT: B 697 MET cc_start: 0.8473 (ptm) cc_final: 0.8068 (ttp) REVERT: C 223 LEU cc_start: 0.9240 (mp) cc_final: 0.8204 (mp) REVERT: C 754 LEU cc_start: 0.9655 (tt) cc_final: 0.9397 (mp) REVERT: C 777 ASN cc_start: 0.9049 (m-40) cc_final: 0.8528 (m110) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1606 time to fit residues: 28.4606 Evaluate side-chains 71 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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: 7.9990 chunk 97 optimal weight: 5.9990 chunk 263 optimal weight: 0.1980 chunk 164 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 chunk 177 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 ASN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.060749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.040540 restraints weight = 168254.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.042030 restraints weight = 89836.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.043029 restraints weight = 59646.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043687 restraints weight = 45100.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.044079 restraints weight = 37421.559| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26137 Z= 0.104 Angle : 0.518 10.566 35645 Z= 0.266 Chirality : 0.043 0.362 4100 Planarity : 0.004 0.062 4562 Dihedral : 4.370 55.012 4124 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3161 helix: 1.39 (0.21), residues: 613 sheet: -0.18 (0.19), residues: 716 loop : -1.39 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C1019 TYR 0.012 0.001 TYR C 904 PHE 0.023 0.001 PHE C 906 TRP 0.011 0.001 TRP C 152 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00229 (26062) covalent geometry : angle 0.51241 (35462) SS BOND : bond 0.00315 ( 42) SS BOND : angle 0.93994 ( 84) hydrogen bonds : bond 0.04131 ( 806) hydrogen bonds : angle 5.02142 ( 2385) link_BETA1-4 : bond 0.00440 ( 1) link_BETA1-4 : angle 1.25931 ( 3) link_NAG-ASN : bond 0.00197 ( 32) link_NAG-ASN : angle 1.41735 ( 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 109 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.928 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 90 VAL cc_start: 0.9366 (p) cc_final: 0.9124 (m) REVERT: A 544 ASN cc_start: 0.9408 (m-40) cc_final: 0.8579 (p0) REVERT: A 1002 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 177 MET cc_start: 0.4050 (ptt) cc_final: 0.3621 (ptp) REVERT: B 697 MET cc_start: 0.8456 (ptm) cc_final: 0.8054 (ttp) REVERT: C 118 LEU cc_start: 0.9165 (mt) cc_final: 0.8957 (mt) REVERT: C 276 LEU cc_start: 0.9445 (tp) cc_final: 0.9179 (tp) REVERT: C 754 LEU cc_start: 0.9652 (tt) cc_final: 0.9400 (mp) REVERT: C 777 ASN cc_start: 0.9063 (m-40) cc_final: 0.8538 (m110) REVERT: C 1005 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8711 (tm-30) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.1619 time to fit residues: 29.9460 Evaluate side-chains 71 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 4.9990 chunk 171 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 52 GLN A 487 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A 955 ASN B 146 HIS B 703 ASN C1064 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.058861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.038863 restraints weight = 172341.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.040786 restraints weight = 97291.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.041396 restraints weight = 54052.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.041700 restraints weight = 42783.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.041842 restraints weight = 39161.251| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 26137 Z= 0.254 Angle : 0.670 10.652 35645 Z= 0.340 Chirality : 0.045 0.286 4100 Planarity : 0.004 0.064 4562 Dihedral : 4.873 55.633 4124 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.43 % 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: -1.08 (0.14), residues: 3161 helix: 0.84 (0.21), residues: 612 sheet: -0.36 (0.19), residues: 738 loop : -1.47 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1019 TYR 0.014 0.002 TYR A1110 PHE 0.028 0.002 PHE A 906 TRP 0.011 0.002 TRP C1102 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00560 (26062) covalent geometry : angle 0.65933 (35462) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.12345 ( 84) hydrogen bonds : bond 0.04912 ( 806) hydrogen bonds : angle 5.46284 ( 2385) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 1.19556 ( 3) link_NAG-ASN : bond 0.00319 ( 32) link_NAG-ASN : angle 2.22127 ( 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 92 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.991 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: 0.9511 (m-40) cc_final: 0.8717 (p0) REVERT: A 1002 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8549 (tm-30) REVERT: B 177 MET cc_start: 0.4414 (ptt) cc_final: 0.4011 (ptp) REVERT: B 697 MET cc_start: 0.8446 (ptm) cc_final: 0.8003 (ttp) REVERT: C 276 LEU cc_start: 0.9554 (tp) cc_final: 0.9291 (tp) REVERT: C 754 LEU cc_start: 0.9670 (tt) cc_final: 0.9421 (mp) REVERT: C 777 ASN cc_start: 0.9125 (m-40) cc_final: 0.8553 (m110) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1730 time to fit residues: 26.9338 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 : 0.972 ------------------------------------------------------------------------------- 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: 7.9990 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN B 146 HIS B 448 ASN B 703 ASN C 245 HIS C 914 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.059760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.039320 restraints weight = 166377.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040844 restraints weight = 86019.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.041846 restraints weight = 56076.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042532 restraints weight = 41965.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.042968 restraints weight = 34654.976| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26137 Z= 0.133 Angle : 0.545 10.550 35645 Z= 0.279 Chirality : 0.043 0.291 4100 Planarity : 0.004 0.059 4562 Dihedral : 4.639 55.754 4124 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % 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: -0.87 (0.14), residues: 3161 helix: 1.23 (0.21), residues: 614 sheet: -0.21 (0.19), residues: 733 loop : -1.42 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.011 0.001 TYR A1067 PHE 0.020 0.001 PHE A 906 TRP 0.011 0.001 TRP C 152 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00294 (26062) covalent geometry : angle 0.53682 (35462) SS BOND : bond 0.00207 ( 42) SS BOND : angle 0.93244 ( 84) hydrogen bonds : bond 0.04333 ( 806) hydrogen bonds : angle 5.14411 ( 2385) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 1.19919 ( 3) link_NAG-ASN : bond 0.00174 ( 32) link_NAG-ASN : angle 1.78992 ( 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 : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.9455 (m-40) cc_final: 0.8650 (p0) REVERT: A 1002 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8607 (tm-30) REVERT: B 177 MET cc_start: 0.4388 (ptt) cc_final: 0.4008 (ptp) REVERT: B 697 MET cc_start: 0.8461 (ptm) cc_final: 0.8033 (ttp) REVERT: B 725 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 118 LEU cc_start: 0.9203 (mt) cc_final: 0.8998 (mt) REVERT: C 777 ASN cc_start: 0.9071 (m-40) cc_final: 0.8518 (m110) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1714 time to fit residues: 27.4070 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 : 1.055 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 137 optimal weight: 0.3980 chunk 299 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 257 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 146 HIS B 703 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.058798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.039026 restraints weight = 170479.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.040656 restraints weight = 93785.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.041856 restraints weight = 52055.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.041934 restraints weight = 42786.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.041933 restraints weight = 36212.937| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 26137 Z= 0.230 Angle : 0.629 11.137 35645 Z= 0.322 Chirality : 0.044 0.270 4100 Planarity : 0.004 0.062 4562 Dihedral : 4.893 55.688 4124 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.68 % 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: 0.89 (0.21), residues: 616 sheet: -0.28 (0.19), residues: 727 loop : -1.50 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.016 0.002 TYR C 266 PHE 0.024 0.002 PHE A 906 TRP 0.018 0.002 TRP C 64 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00507 (26062) covalent geometry : angle 0.62117 (35462) SS BOND : bond 0.00296 ( 42) SS BOND : angle 1.00286 ( 84) hydrogen bonds : bond 0.04798 ( 806) hydrogen bonds : angle 5.41259 ( 2385) link_BETA1-4 : bond 0.00012 ( 1) link_BETA1-4 : angle 1.33357 ( 3) link_NAG-ASN : bond 0.00271 ( 32) link_NAG-ASN : angle 1.81501 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.23 seconds wall clock time: 83 minutes 16.16 seconds (4996.16 seconds total)