Starting phenix.real_space_refine on Sun Jul 5 05:06:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yqu_34035/07_2026/7yqu_34035.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.103 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 16305 2.51 5 N 4209 2.21 5 O 4959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25587 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.66, per 1000 atoms: 0.22 Number of scatterers: 25587 At special positions: 0 Unit cell: (143.38, 151.94, 173.34, 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 4959 8.00 N 4209 7.00 C 16305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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 C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.03 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 617 " - pdb=" SG CYS B 649 " distance=2.03 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 B 840 " - pdb=" SG CYS B 851 " 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 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 785.1 milliseconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 21.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.765A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.695A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 822 removed outlier: 3.884A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 817 through 822' Processing helix chain 'C' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP C 843 " --> pdb=" O CYS C 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 840 through 844' Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 869 through 880 Processing helix 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 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.638A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.699A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.765A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.694A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 819 Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 844' Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 869 through 880 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.638A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.699A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.766A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.694A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 822 removed outlier: 3.660A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP B 843 " --> pdb=" O CYS B 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 840 through 844' Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 869 through 880 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.637A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.698A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.953A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.537A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 107 removed outlier: 3.679A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.849A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.711A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.787A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.783A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.645A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.952A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.536A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.848A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.788A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.594A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.646A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.953A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 101 through 107 removed outlier: 3.679A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.849A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.788A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AE9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.645A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'B' and resid 1094 through 1097 802 hydrogen bonds defined for protein. 2193 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: 5.40 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4141 1.31 - 1.44: 7343 1.44 - 1.57: 14553 1.57 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 26178 Sorted by residual: bond pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta sigma weight residual 1.469 1.435 0.034 7.40e-03 1.83e+04 2.10e+01 bond pdb=" C PRO A 373 " pdb=" O PRO A 373 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.57e+01 bond pdb=" C PRO B 373 " pdb=" O PRO B 373 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" CA ALA C 372 " pdb=" CB ALA C 372 " ideal model delta sigma weight residual 1.530 1.471 0.058 1.58e-02 4.01e+03 1.36e+01 bond pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta sigma weight residual 1.469 1.423 0.045 1.28e-02 6.10e+03 1.26e+01 ... (remaining 26173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 35532 4.24 - 8.49: 97 8.49 - 12.73: 6 12.73 - 16.98: 0 16.98 - 21.22: 2 Bond angle restraints: 35637 Sorted by residual: angle pdb=" C PHE B 377 " pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " ideal model delta sigma weight residual 110.79 89.57 21.22 1.63e+00 3.76e-01 1.70e+02 angle pdb=" C PHE C 377 " pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta sigma weight residual 111.68 90.93 20.75 1.68e+00 3.54e-01 1.53e+02 angle pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " pdb=" CG PHE B 377 " ideal model delta sigma weight residual 113.80 122.65 -8.85 1.00e+00 1.00e+00 7.83e+01 angle pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " pdb=" CG PHE C 377 " ideal model delta sigma weight residual 113.80 122.37 -8.57 1.00e+00 1.00e+00 7.34e+01 angle pdb=" C PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta sigma weight residual 109.80 97.27 12.53 1.64e+00 3.72e-01 5.84e+01 ... (remaining 35632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13699 17.99 - 35.99: 1225 35.99 - 53.98: 235 53.98 - 71.97: 24 71.97 - 89.97: 36 Dihedral angle restraints: 15219 sinusoidal: 5931 harmonic: 9288 Sorted by residual: dihedral pdb=" C PHE B 377 " pdb=" N PHE B 377 " pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " ideal model delta harmonic sigma weight residual -122.60 -97.22 -25.38 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" C PHE C 377 " pdb=" N PHE C 377 " pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta harmonic sigma weight residual -122.60 -99.91 -22.69 0 2.50e+00 1.60e-01 8.24e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 29.30 63.70 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 15216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3837 0.092 - 0.185: 321 0.185 - 0.277: 3 0.277 - 0.370: 3 0.370 - 0.462: 3 Chirality restraints: 4167 Sorted by residual: chirality pdb=" CA PHE B 377 " pdb=" N PHE B 377 " pdb=" C PHE B 377 " pdb=" CB PHE B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA PHE C 377 " pdb=" N PHE C 377 " pdb=" C PHE C 377 " pdb=" CB PHE C 377 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 4164 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 372 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C ALA A 372 " -0.073 2.00e-02 2.50e+03 pdb=" O ALA A 372 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 373 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 372 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ALA B 372 " 0.066 2.00e-02 2.50e+03 pdb=" O ALA B 372 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 373 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 818 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ILE C 818 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE C 818 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU C 819 " 0.022 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 7558 2.81 - 3.51: 30387 3.51 - 4.20: 53037 4.20 - 4.90: 99490 Nonbonded interactions: 190475 Sorted by model distance: nonbonded pdb=" NH2 ARG C 847 " pdb=" OD2 ASP A 568 " model vdw 1.425 3.120 nonbonded pdb=" NH2 ARG A 847 " pdb=" OD2 ASP B 568 " model vdw 1.443 3.120 nonbonded pdb=" OD2 ASP C 568 " pdb=" NH2 ARG B 847 " model vdw 1.445 3.120 nonbonded pdb=" CG1 VAL C1094 " pdb=" OH TYR B 904 " model vdw 2.160 3.460 nonbonded pdb=" OH TYR A 904 " pdb=" CG1 VAL B1094 " model vdw 2.180 3.460 ... (remaining 190470 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.560 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.005 0.058 26265 Z= 0.241 Angle : 0.737 21.223 35859 Z= 0.396 Chirality : 0.050 0.462 4167 Planarity : 0.004 0.042 4563 Dihedral : 14.270 89.966 9132 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.48 % Favored : 91.48 % Rotamer: Outliers : 0.14 % Allowed : 0.22 % Favored : 99.64 % Cbeta Deviations : 0.20 % 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: -1.47 (0.14), residues: 3159 helix: 0.28 (0.22), residues: 609 sheet: 0.29 (0.20), residues: 630 loop : -1.95 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.047 0.002 TYR A 495 PHE 0.028 0.002 PHE A 906 TRP 0.012 0.002 TRP A 64 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (26178) covalent geometry : angle 0.71640 / 0.39 (35637) SS BOND : bond 0.00366 / 0.22 ( 39) SS BOND : angle 1.73186 / 1.06 ( 78) hydrogen bonds : bond 0.15713 / 10.40 ( 802) hydrogen bonds : angle 6.84116 / 4.78 ( 2193) link_BETA1-4 : bond 0.00661 / 0.37 ( 6) link_BETA1-4 : angle 0.98911 / 0.59 ( 18) link_NAG-ASN : bond 0.00575 / 0.46 ( 42) link_NAG-ASN : angle 2.72564 / 1.68 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.642 Fit side-chains REVERT: C 375 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: C 934 ILE cc_start: 0.9094 (tt) cc_final: 0.8893 (tt) REVERT: C 1050 MET cc_start: 0.8291 (mtp) cc_final: 0.8057 (mtp) REVERT: A 375 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: A 1138 TYR cc_start: 0.7551 (m-80) cc_final: 0.7270 (t80) REVERT: B 375 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 428 ASP cc_start: 0.7994 (p0) cc_final: 0.7749 (p0) REVERT: B 985 ASP cc_start: 0.8294 (p0) cc_final: 0.7995 (p0) REVERT: B 1072 GLU cc_start: 0.8106 (pm20) cc_final: 0.7784 (pm20) outliers start: 4 outliers final: 0 residues processed: 212 average time/residue: 0.1517 time to fit residues: 51.8100 Evaluate side-chains 166 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094586 restraints weight = 35630.957| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.93 r_work: 0.2936 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26265 Z= 0.123 Angle : 0.592 12.167 35859 Z= 0.295 Chirality : 0.045 0.341 4167 Planarity : 0.004 0.065 4563 Dihedral : 4.715 55.417 3432 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.79 % Allowed : 6.13 % Favored : 93.07 % 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: -1.20 (0.15), residues: 3159 helix: 0.73 (0.22), residues: 615 sheet: 0.55 (0.20), residues: 660 loop : -1.95 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.032 0.001 TYR A 495 PHE 0.014 0.001 PHE B 135 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (26178) covalent geometry : angle 0.56948 / 0.29 (35637) SS BOND : bond 0.00248 / 0.15 ( 39) SS BOND : angle 1.21226 / 0.75 ( 78) hydrogen bonds : bond 0.05495 / 3.69 ( 802) hydrogen bonds : angle 5.26132 / 3.67 ( 2193) link_BETA1-4 : bond 0.00428 / 0.23 ( 6) link_BETA1-4 : angle 0.78065 / 0.50 ( 18) link_NAG-ASN : bond 0.00573 / 0.45 ( 42) link_NAG-ASN : angle 2.64901 / 1.61 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.964 Fit side-chains REVERT: C 375 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: C 1072 GLU cc_start: 0.8644 (pm20) cc_final: 0.8336 (pm20) REVERT: A 134 GLN cc_start: 0.6912 (tm130) cc_final: 0.6629 (tm-30) REVERT: A 574 ASP cc_start: 0.8601 (t0) cc_final: 0.8313 (t0) REVERT: A 869 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8053 (ptp) REVERT: A 1138 TYR cc_start: 0.7756 (m-80) cc_final: 0.6910 (t80) REVERT: B 375 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: B 377 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7364 (m-10) REVERT: B 1072 GLU cc_start: 0.8653 (pm20) cc_final: 0.8270 (pm20) outliers start: 22 outliers final: 16 residues processed: 181 average time/residue: 0.1681 time to fit residues: 49.7607 Evaluate side-chains 175 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 75 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN C 317 ASN C 506 GLN C1119 ASN A 207 HIS A 506 GLN A1125 ASN B 134 GLN B 207 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.096031 restraints weight = 35656.121| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.93 r_work: 0.2940 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26265 Z= 0.117 Angle : 0.561 12.065 35859 Z= 0.278 Chirality : 0.045 0.336 4167 Planarity : 0.004 0.060 4563 Dihedral : 4.485 52.973 3432 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.05 % Allowed : 8.30 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3159 helix: 0.93 (0.23), residues: 615 sheet: 0.64 (0.20), residues: 660 loop : -1.88 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.026 0.001 TYR A 495 PHE 0.012 0.001 PHE B 906 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (26178) covalent geometry : angle 0.53888 / 0.27 (35637) SS BOND : bond 0.00193 / 0.12 ( 39) SS BOND : angle 1.07594 / 0.67 ( 78) hydrogen bonds : bond 0.04995 / 3.36 ( 802) hydrogen bonds : angle 4.96386 / 3.45 ( 2193) link_BETA1-4 : bond 0.00442 / 0.24 ( 6) link_BETA1-4 : angle 0.83113 / 0.52 ( 18) link_NAG-ASN : bond 0.00537 / 0.43 ( 42) link_NAG-ASN : angle 2.55337 / 1.54 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.052 Fit side-chains REVERT: C 375 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: C 646 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7957 (mpp80) REVERT: C 1072 GLU cc_start: 0.8660 (pm20) cc_final: 0.8367 (pm20) REVERT: A 134 GLN cc_start: 0.7030 (tm130) cc_final: 0.6486 (tm-30) REVERT: A 574 ASP cc_start: 0.8610 (t0) cc_final: 0.8127 (t0) REVERT: A 1138 TYR cc_start: 0.7637 (m-80) cc_final: 0.6950 (t80) REVERT: B 375 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: B 1072 GLU cc_start: 0.8658 (pm20) cc_final: 0.8277 (pm20) REVERT: B 1138 TYR cc_start: 0.7651 (t80) cc_final: 0.7449 (t80) outliers start: 29 outliers final: 15 residues processed: 191 average time/residue: 0.1666 time to fit residues: 52.0702 Evaluate side-chains 172 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 211 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 0.0570 chunk 285 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN A 207 HIS B 134 GLN B 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.093852 restraints weight = 35391.216| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.82 r_work: 0.2923 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26265 Z= 0.142 Angle : 0.575 11.774 35859 Z= 0.287 Chirality : 0.045 0.333 4167 Planarity : 0.004 0.056 4563 Dihedral : 4.526 52.793 3432 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.44 % Allowed : 9.38 % Favored : 89.18 % 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 (0.15), residues: 3159 helix: 0.96 (0.23), residues: 612 sheet: 0.69 (0.20), residues: 654 loop : -1.94 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.028 0.001 TYR C 495 PHE 0.018 0.001 PHE C 906 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (26178) covalent geometry : angle 0.55392 / 0.28 (35637) SS BOND : bond 0.00243 / 0.14 ( 39) SS BOND : angle 1.15654 / 0.72 ( 78) hydrogen bonds : bond 0.05322 / 3.58 ( 802) hydrogen bonds : angle 4.89138 / 3.38 ( 2193) link_BETA1-4 : bond 0.00416 / 0.23 ( 6) link_BETA1-4 : angle 0.79998 / 0.50 ( 18) link_NAG-ASN : bond 0.00506 / 0.40 ( 42) link_NAG-ASN : angle 2.51812 / 1.53 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.981 Fit side-chains REVERT: C 375 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: C 495 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.5657 (t80) REVERT: C 1072 GLU cc_start: 0.8691 (pm20) cc_final: 0.8436 (pm20) REVERT: A 134 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: A 212 LEU cc_start: 0.4199 (OUTLIER) cc_final: 0.3781 (tp) REVERT: A 574 ASP cc_start: 0.8610 (t0) cc_final: 0.8120 (t0) REVERT: A 1138 TYR cc_start: 0.7470 (m-80) cc_final: 0.7034 (t80) REVERT: B 212 LEU cc_start: 0.4334 (OUTLIER) cc_final: 0.4023 (tp) REVERT: B 495 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.6373 (t80) REVERT: B 649 CYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8235 (p) REVERT: B 900 MET cc_start: 0.8977 (mtp) cc_final: 0.8767 (mtm) REVERT: B 1072 GLU cc_start: 0.8660 (pm20) cc_final: 0.8232 (pm20) outliers start: 40 outliers final: 20 residues processed: 199 average time/residue: 0.1485 time to fit residues: 49.5237 Evaluate side-chains 186 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 114 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 0.0070 chunk 168 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN A 207 HIS A 505 HIS A1005 GLN B 134 GLN B 207 HIS B 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092076 restraints weight = 35560.079| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.82 r_work: 0.2894 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26265 Z= 0.189 Angle : 0.614 11.535 35859 Z= 0.307 Chirality : 0.047 0.334 4167 Planarity : 0.004 0.054 4563 Dihedral : 4.547 53.583 3428 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.88 % Allowed : 10.57 % Favored : 87.55 % 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: -1.22 (0.15), residues: 3159 helix: 0.84 (0.22), residues: 612 sheet: 0.60 (0.20), residues: 654 loop : -2.02 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.039 0.002 TYR A 495 PHE 0.022 0.002 PHE B 906 TRP 0.013 0.002 TRP C 633 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (26178) covalent geometry : angle 0.59358 / 0.30 (35637) SS BOND : bond 0.00301 / 0.18 ( 39) SS BOND : angle 1.36495 / 0.85 ( 78) hydrogen bonds : bond 0.06010 / 4.04 ( 802) hydrogen bonds : angle 4.98963 / 3.44 ( 2193) link_BETA1-4 : bond 0.00457 / 0.25 ( 6) link_BETA1-4 : angle 0.83651 / 0.51 ( 18) link_NAG-ASN : bond 0.00512 / 0.40 ( 42) link_NAG-ASN : angle 2.55091 / 1.56 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.956 Fit side-chains REVERT: C 375 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: C 495 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.6297 (t80) REVERT: C 1072 GLU cc_start: 0.8709 (pm20) cc_final: 0.8433 (pm20) REVERT: A 134 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: A 212 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.4004 (tp) REVERT: A 574 ASP cc_start: 0.8610 (t0) cc_final: 0.8115 (t0) REVERT: A 1138 TYR cc_start: 0.7469 (m-80) cc_final: 0.7007 (t80) REVERT: B 177 MET cc_start: 0.4551 (mmt) cc_final: 0.4206 (mmt) REVERT: B 212 LEU cc_start: 0.4424 (OUTLIER) cc_final: 0.4096 (tp) REVERT: B 375 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 495 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6256 (t80) REVERT: B 900 MET cc_start: 0.8955 (mtp) cc_final: 0.8750 (mtm) REVERT: B 1072 GLU cc_start: 0.8700 (pm20) cc_final: 0.8267 (pm20) outliers start: 52 outliers final: 35 residues processed: 198 average time/residue: 0.1565 time to fit residues: 51.7495 Evaluate side-chains 195 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 211 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN A 207 HIS A1005 GLN B 134 GLN B 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093561 restraints weight = 35646.482| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.83 r_work: 0.2917 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26265 Z= 0.128 Angle : 0.564 11.243 35859 Z= 0.282 Chirality : 0.045 0.331 4167 Planarity : 0.004 0.052 4563 Dihedral : 4.393 53.001 3428 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.70 % Allowed : 12.30 % Favored : 86.00 % 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: -1.10 (0.15), residues: 3159 helix: 0.95 (0.23), residues: 615 sheet: 0.66 (0.20), residues: 654 loop : -1.96 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.028 0.001 TYR C 495 PHE 0.013 0.001 PHE B 906 TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (26178) covalent geometry : angle 0.54405 / 0.28 (35637) SS BOND : bond 0.00222 / 0.13 ( 39) SS BOND : angle 1.05965 / 0.67 ( 78) hydrogen bonds : bond 0.05166 / 3.47 ( 802) hydrogen bonds : angle 4.86142 / 3.36 ( 2193) link_BETA1-4 : bond 0.00437 / 0.24 ( 6) link_BETA1-4 : angle 0.78210 / 0.49 ( 18) link_NAG-ASN : bond 0.00505 / 0.40 ( 42) link_NAG-ASN : angle 2.48354 / 1.51 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.978 Fit side-chains REVERT: C 375 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: C 495 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6199 (t80) REVERT: C 1072 GLU cc_start: 0.8694 (pm20) cc_final: 0.8439 (pm20) REVERT: A 134 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: A 212 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.3887 (tp) REVERT: A 574 ASP cc_start: 0.8576 (t0) cc_final: 0.8093 (t0) REVERT: A 1138 TYR cc_start: 0.7432 (m-80) cc_final: 0.7015 (t80) REVERT: B 177 MET cc_start: 0.4542 (mmt) cc_final: 0.4197 (mmt) REVERT: B 212 LEU cc_start: 0.4398 (OUTLIER) cc_final: 0.4082 (tp) REVERT: B 375 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 495 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.6250 (t80) REVERT: B 574 ASP cc_start: 0.8592 (t0) cc_final: 0.8385 (t0) REVERT: B 649 CYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8235 (p) REVERT: B 900 MET cc_start: 0.8932 (mtp) cc_final: 0.8724 (mtm) REVERT: B 1072 GLU cc_start: 0.8660 (pm20) cc_final: 0.8238 (pm20) outliers start: 47 outliers final: 30 residues processed: 201 average time/residue: 0.1572 time to fit residues: 52.8682 Evaluate side-chains 197 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 180 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 106 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN C 207 HIS A 207 HIS A1005 GLN B 134 GLN B 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091701 restraints weight = 35631.329| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.81 r_work: 0.2888 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26265 Z= 0.191 Angle : 0.618 11.132 35859 Z= 0.308 Chirality : 0.047 0.330 4167 Planarity : 0.004 0.051 4563 Dihedral : 4.574 53.420 3428 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 1.77 % Allowed : 13.02 % Favored : 85.21 % 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: -1.23 (0.15), residues: 3159 helix: 0.86 (0.22), residues: 612 sheet: 0.57 (0.20), residues: 654 loop : -2.04 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.039 0.001 TYR C 495 PHE 0.019 0.002 PHE C 86 TRP 0.014 0.002 TRP A 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (26178) covalent geometry : angle 0.59764 / 0.30 (35637) SS BOND : bond 0.00309 / 0.18 ( 39) SS BOND : angle 1.33495 / 0.83 ( 78) hydrogen bonds : bond 0.06027 / 4.05 ( 802) hydrogen bonds : angle 4.97656 / 3.43 ( 2193) link_BETA1-4 : bond 0.00480 / 0.26 ( 6) link_BETA1-4 : angle 0.84848 / 0.52 ( 18) link_NAG-ASN : bond 0.00499 / 0.39 ( 42) link_NAG-ASN : angle 2.51366 / 1.54 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.002 Fit side-chains REVERT: C 375 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: C 433 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8637 (t) REVERT: C 495 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.6643 (t80) REVERT: C 787 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: C 1072 GLU cc_start: 0.8708 (pm20) cc_final: 0.8429 (pm20) REVERT: A 134 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: A 212 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4056 (tp) REVERT: A 574 ASP cc_start: 0.8602 (t0) cc_final: 0.8104 (t0) REVERT: A 1138 TYR cc_start: 0.7454 (m-80) cc_final: 0.7027 (t80) REVERT: B 177 MET cc_start: 0.4689 (mmt) cc_final: 0.4371 (mmt) REVERT: B 212 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3954 (tp) REVERT: B 375 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: B 495 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6202 (t80) REVERT: B 900 MET cc_start: 0.8959 (mtp) cc_final: 0.8741 (mtm) REVERT: B 1072 GLU cc_start: 0.8704 (pm20) cc_final: 0.8285 (pm20) outliers start: 49 outliers final: 30 residues processed: 191 average time/residue: 0.1582 time to fit residues: 50.3369 Evaluate side-chains 184 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 180 optimal weight: 4.9990 chunk 315 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 206 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 HIS A 207 HIS B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094758 restraints weight = 35517.625| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.83 r_work: 0.2941 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26265 Z= 0.105 Angle : 0.545 10.767 35859 Z= 0.270 Chirality : 0.044 0.328 4167 Planarity : 0.004 0.050 4563 Dihedral : 4.261 52.379 3428 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.26 % Allowed : 13.74 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 3159 helix: 1.06 (0.23), residues: 615 sheet: 0.79 (0.22), residues: 582 loop : -1.87 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.023 0.001 TYR C 495 PHE 0.012 0.001 PHE C 135 TRP 0.013 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (26178) covalent geometry : angle 0.52572 / 0.27 (35637) SS BOND : bond 0.00242 / 0.17 ( 39) SS BOND : angle 0.91504 / 0.59 ( 78) hydrogen bonds : bond 0.04599 / 3.09 ( 802) hydrogen bonds : angle 4.76108 / 3.29 ( 2193) link_BETA1-4 : bond 0.00430 / 0.23 ( 6) link_BETA1-4 : angle 0.77968 / 0.50 ( 18) link_NAG-ASN : bond 0.00495 / 0.39 ( 42) link_NAG-ASN : angle 2.38875 / 1.46 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.095 Fit side-chains REVERT: C 375 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: C 495 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6119 (t80) REVERT: C 787 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: C 902 MET cc_start: 0.9032 (tpp) cc_final: 0.8573 (mmm) REVERT: C 1072 GLU cc_start: 0.8702 (pm20) cc_final: 0.8468 (pm20) REVERT: A 134 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: A 212 LEU cc_start: 0.4219 (OUTLIER) cc_final: 0.3834 (tp) REVERT: A 574 ASP cc_start: 0.8560 (t0) cc_final: 0.8125 (t0) REVERT: A 1138 TYR cc_start: 0.7511 (m-80) cc_final: 0.7137 (t80) REVERT: B 177 MET cc_start: 0.4758 (mmt) cc_final: 0.4456 (mmt) REVERT: B 212 LEU cc_start: 0.4387 (OUTLIER) cc_final: 0.4092 (tp) REVERT: B 375 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: B 495 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6118 (t80) REVERT: B 649 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 900 MET cc_start: 0.8902 (mtp) cc_final: 0.8691 (mtm) REVERT: B 1072 GLU cc_start: 0.8674 (pm20) cc_final: 0.8313 (pm20) outliers start: 35 outliers final: 21 residues processed: 185 average time/residue: 0.1556 time to fit residues: 48.7108 Evaluate side-chains 186 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 3 optimal weight: 0.0000 chunk 282 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 HIS A 207 HIS B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.095375 restraints weight = 35521.057| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.83 r_work: 0.2950 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26265 Z= 0.102 Angle : 0.537 10.376 35859 Z= 0.266 Chirality : 0.044 0.327 4167 Planarity : 0.004 0.049 4563 Dihedral : 4.106 51.841 3428 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.48 % Allowed : 13.82 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3159 helix: 1.10 (0.23), residues: 621 sheet: 0.55 (0.21), residues: 648 loop : -1.82 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 646 TYR 0.023 0.001 TYR C 495 PHE 0.013 0.001 PHE C 135 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (26178) covalent geometry : angle 0.51939 / 0.26 (35637) SS BOND : bond 0.00196 / 0.11 ( 39) SS BOND : angle 0.93769 / 0.60 ( 78) hydrogen bonds : bond 0.04425 / 2.98 ( 802) hydrogen bonds : angle 4.63990 / 3.21 ( 2193) link_BETA1-4 : bond 0.00396 / 0.22 ( 6) link_BETA1-4 : angle 0.79920 / 0.50 ( 18) link_NAG-ASN : bond 0.00479 / 0.38 ( 42) link_NAG-ASN : angle 2.27357 / 1.38 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.910 Fit side-chains REVERT: C 134 GLN cc_start: 0.6906 (tm-30) cc_final: 0.6655 (tm-30) REVERT: C 375 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: C 495 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6137 (t80) REVERT: C 787 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: C 1072 GLU cc_start: 0.8740 (pm20) cc_final: 0.8510 (pm20) REVERT: C 1138 TYR cc_start: 0.7270 (t80) cc_final: 0.7064 (t80) REVERT: A 134 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: A 212 LEU cc_start: 0.4144 (OUTLIER) cc_final: 0.3772 (tp) REVERT: A 529 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7406 (mmtp) REVERT: A 574 ASP cc_start: 0.8514 (t0) cc_final: 0.8025 (t0) REVERT: A 632 THR cc_start: 0.7260 (p) cc_final: 0.6983 (p) REVERT: A 1138 TYR cc_start: 0.7521 (m-80) cc_final: 0.7113 (t80) REVERT: B 177 MET cc_start: 0.4741 (mmt) cc_final: 0.4442 (mmt) REVERT: B 212 LEU cc_start: 0.4509 (OUTLIER) cc_final: 0.4092 (tp) REVERT: B 375 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 495 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.6091 (t80) REVERT: B 649 CYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 900 MET cc_start: 0.8919 (mtp) cc_final: 0.8620 (mtp) REVERT: B 1072 GLU cc_start: 0.8681 (pm20) cc_final: 0.8340 (pm20) outliers start: 41 outliers final: 26 residues processed: 197 average time/residue: 0.1424 time to fit residues: 46.8503 Evaluate side-chains 196 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 243 optimal weight: 0.0060 chunk 185 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 HIS A 207 HIS B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097356 restraints weight = 35627.617| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.93 r_work: 0.2964 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26265 Z= 0.094 Angle : 0.530 10.861 35859 Z= 0.261 Chirality : 0.044 0.324 4167 Planarity : 0.004 0.048 4563 Dihedral : 3.995 51.441 3428 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.23 % Allowed : 14.18 % Favored : 84.60 % 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: -0.93 (0.15), residues: 3159 helix: 1.18 (0.23), residues: 621 sheet: 0.61 (0.22), residues: 582 loop : -1.72 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.019 0.001 TYR C 495 PHE 0.012 0.001 PHE B 135 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (26178) covalent geometry : angle 0.51362 / 0.26 (35637) SS BOND : bond 0.00136 / 0.08 ( 39) SS BOND : angle 0.79985 / 0.52 ( 78) hydrogen bonds : bond 0.04078 / 2.74 ( 802) hydrogen bonds : angle 4.55659 / 3.15 ( 2193) link_BETA1-4 : bond 0.00407 / 0.22 ( 6) link_BETA1-4 : angle 0.79991 / 0.51 ( 18) link_NAG-ASN : bond 0.00474 / 0.37 ( 42) link_NAG-ASN : angle 2.17899 / 1.33 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.751 Fit side-chains REVERT: C 134 GLN cc_start: 0.6848 (tm-30) cc_final: 0.6588 (tm-30) REVERT: C 375 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: C 495 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.5867 (t80) REVERT: C 787 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: C 1138 TYR cc_start: 0.7285 (t80) cc_final: 0.7060 (t80) REVERT: A 134 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6351 (tm-30) REVERT: A 212 LEU cc_start: 0.4044 (OUTLIER) cc_final: 0.3684 (tp) REVERT: A 529 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7447 (mmtp) REVERT: A 574 ASP cc_start: 0.8451 (t0) cc_final: 0.7940 (t0) REVERT: A 1138 TYR cc_start: 0.7516 (m-80) cc_final: 0.7046 (t80) REVERT: B 134 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6847 (tm-30) REVERT: B 177 MET cc_start: 0.4698 (mmt) cc_final: 0.4393 (mmt) REVERT: B 212 LEU cc_start: 0.4454 (OUTLIER) cc_final: 0.4049 (tp) REVERT: B 375 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: B 495 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6047 (t80) REVERT: B 649 CYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 1072 GLU cc_start: 0.8684 (pm20) cc_final: 0.8392 (pm20) outliers start: 34 outliers final: 21 residues processed: 193 average time/residue: 0.1411 time to fit residues: 46.0076 Evaluate side-chains 196 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 105 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 159 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 HIS A 134 GLN A 207 HIS B 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095600 restraints weight = 35532.646| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.93 r_work: 0.2949 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26265 Z= 0.106 Angle : 0.536 9.854 35859 Z= 0.264 Chirality : 0.044 0.323 4167 Planarity : 0.004 0.048 4563 Dihedral : 3.998 51.504 3428 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.26 % Allowed : 14.32 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3159 helix: 1.18 (0.23), residues: 621 sheet: 0.68 (0.22), residues: 576 loop : -1.73 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.024 0.001 TYR C 495 PHE 0.013 0.001 PHE B 135 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (26178) covalent geometry : angle 0.52016 / 0.26 (35637) SS BOND : bond 0.00157 / 0.10 ( 39) SS BOND : angle 0.89538 / 0.57 ( 78) hydrogen bonds : bond 0.04354 / 2.93 ( 802) hydrogen bonds : angle 4.55592 / 3.15 ( 2193) link_BETA1-4 : bond 0.00420 / 0.23 ( 6) link_BETA1-4 : angle 0.81095 / 0.51 ( 18) link_NAG-ASN : bond 0.00460 / 0.37 ( 42) link_NAG-ASN : angle 2.14692 / 1.31 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4733.05 seconds wall clock time: 82 minutes 20.71 seconds (4940.71 seconds total)