Starting phenix.real_space_refine on Mon Aug 25 06:01:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqu_34035/08_2025/7yqu_34035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqu_34035/08_2025/7yqu_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_34035/08_2025/7yqu_34035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqu_34035/08_2025/7yqu_34035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqu_34035/08_2025/7yqu_34035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqu_34035/08_2025/7yqu_34035.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 36 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 dihedrals: 36 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.64, 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.93 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: 5.65 Time building geometry restraints manager: 2.72 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: 14602 17.99 - 35.99: 1300 35.99 - 53.98: 256 53.98 - 71.97: 33 71.97 - 89.97: 36 Dihedral angle restraints: 16227 sinusoidal: 6939 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 16224 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.050 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 14.037 89.966 10140 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 aren 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 covalent geometry : bond 0.00510 (26178) covalent geometry : angle 0.71640 (35637) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.73186 ( 78) hydrogen bonds : bond 0.15713 ( 802) hydrogen bonds : angle 6.84116 ( 2193) link_BETA1-4 : bond 0.00661 ( 6) link_BETA1-4 : angle 0.98911 ( 18) link_NAG-ASN : bond 0.00575 ( 42) link_NAG-ASN : angle 2.72564 ( 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 : 0.827 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: 0.1556 time to fit residues: 53.6580 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 : 1.067 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN 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 ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094878 restraints weight = 35643.326| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.93 r_work: 0.2939 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26265 Z= 0.122 Angle : 0.591 12.070 35859 Z= 0.294 Chirality : 0.046 0.346 4167 Planarity : 0.004 0.067 4563 Dihedral : 6.179 56.857 4440 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.87 % Allowed : 5.99 % Favored : 93.15 % 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 aren not related in a simple way. whole: -1.20 (0.15), residues: 3159 helix: 0.73 (0.23), residues: 615 sheet: 0.56 (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 0.013 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 covalent geometry : bond 0.00276 (26178) covalent geometry : angle 0.56744 (35637) SS BOND : bond 0.00234 ( 39) SS BOND : angle 1.19542 ( 78) hydrogen bonds : bond 0.05369 ( 802) hydrogen bonds : angle 5.24461 ( 2193) link_BETA1-4 : bond 0.00470 ( 6) link_BETA1-4 : angle 0.91681 ( 18) link_NAG-ASN : bond 0.00580 ( 42) link_NAG-ASN : angle 2.67814 ( 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 196 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.912 Fit side-chains REVERT: C 375 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: C 1072 GLU cc_start: 0.8651 (pm20) cc_final: 0.8347 (pm20) REVERT: A 134 GLN cc_start: 0.6915 (tm130) cc_final: 0.6623 (tm-30) REVERT: A 574 ASP cc_start: 0.8604 (t0) cc_final: 0.8319 (t0) REVERT: A 1138 TYR cc_start: 0.7759 (m-80) cc_final: 0.6916 (t80) REVERT: B 375 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: B 1072 GLU cc_start: 0.8658 (pm20) cc_final: 0.8283 (pm20) outliers start: 24 outliers final: 17 residues processed: 184 average time/residue: 0.1488 time to fit residues: 44.9726 Evaluate side-chains 172 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 988 GLU 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 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 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: 3.9990 chunk 109 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 317 ASN A 207 HIS A1125 ASN 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 = 0.3542 r_free = 0.3542 target = 0.128879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.096749 restraints weight = 35639.781| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.93 r_work: 0.2950 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1046 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= 0.107 Angle : 0.549 12.141 35859 Z= 0.272 Chirality : 0.045 0.343 4167 Planarity : 0.004 0.059 4563 Dihedral : 5.387 56.449 4440 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.87 % Allowed : 8.48 % 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 aren not related in a simple way. whole: -1.01 (0.15), residues: 3159 helix: 0.96 (0.23), residues: 615 sheet: 0.68 (0.20), residues: 660 loop : -1.86 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 646 TYR 0.024 0.001 TYR C 495 PHE 0.013 0.001 PHE B 906 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00239 (26178) covalent geometry : angle 0.52542 (35637) SS BOND : bond 0.00178 ( 39) SS BOND : angle 1.02972 ( 78) hydrogen bonds : bond 0.04729 ( 802) hydrogen bonds : angle 4.89133 ( 2193) link_BETA1-4 : bond 0.00488 ( 6) link_BETA1-4 : angle 0.98181 ( 18) link_NAG-ASN : bond 0.00554 ( 42) link_NAG-ASN : angle 2.62605 ( 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 197 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.889 Fit side-chains REVERT: C 375 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: C 1072 GLU cc_start: 0.8700 (pm20) cc_final: 0.8448 (pm20) REVERT: A 134 GLN cc_start: 0.6942 (tm130) cc_final: 0.6543 (tm-30) REVERT: A 574 ASP cc_start: 0.8589 (t0) cc_final: 0.8112 (t0) REVERT: A 1138 TYR cc_start: 0.7473 (m-80) cc_final: 0.6931 (t80) REVERT: B 375 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: B 755 GLN cc_start: 0.8172 (mt0) cc_final: 0.7970 (mt0) REVERT: B 1072 GLU cc_start: 0.8659 (pm20) cc_final: 0.8271 (pm20) outliers start: 24 outliers final: 14 residues processed: 190 average time/residue: 0.1466 time to fit residues: 45.8864 Evaluate side-chains 173 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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 705 VAL 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: 7.9990 chunk 96 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN A 207 HIS A 506 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 = 0.3511 r_free = 0.3511 target = 0.126469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094549 restraints weight = 35410.400| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.84 r_work: 0.2940 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1097 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= 0.129 Angle : 0.562 11.735 35859 Z= 0.279 Chirality : 0.045 0.342 4167 Planarity : 0.004 0.056 4563 Dihedral : 5.137 56.534 4438 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.33 % Allowed : 9.67 % Favored : 89.00 % 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 aren not related in a simple way. whole: -1.03 (0.15), residues: 3159 helix: 0.99 (0.23), residues: 615 sheet: 0.68 (0.20), residues: 660 loop : -1.90 (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 C 495 PHE 0.017 0.001 PHE C 906 TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00307 (26178) covalent geometry : angle 0.53970 (35637) SS BOND : bond 0.00222 ( 39) SS BOND : angle 1.07791 ( 78) hydrogen bonds : bond 0.05060 ( 802) hydrogen bonds : angle 4.82726 ( 2193) link_BETA1-4 : bond 0.00389 ( 6) link_BETA1-4 : angle 0.92765 ( 18) link_NAG-ASN : bond 0.00520 ( 42) link_NAG-ASN : angle 2.57640 ( 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 206 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.966 Fit side-chains REVERT: C 375 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: C 495 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.5724 (t80) REVERT: C 646 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7975 (mpp80) REVERT: C 1072 GLU cc_start: 0.8686 (pm20) cc_final: 0.8423 (pm20) REVERT: A 134 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6362 (tm-30) REVERT: A 212 LEU cc_start: 0.4140 (OUTLIER) cc_final: 0.3743 (tp) REVERT: A 574 ASP cc_start: 0.8607 (t0) cc_final: 0.8170 (t0) REVERT: A 1138 TYR cc_start: 0.7466 (m-80) cc_final: 0.7038 (t80) REVERT: B 212 LEU cc_start: 0.4302 (OUTLIER) cc_final: 0.3993 (tp) REVERT: B 495 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6229 (t80) REVERT: B 649 CYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8268 (p) REVERT: B 755 GLN cc_start: 0.8191 (mt0) cc_final: 0.7983 (mt0) REVERT: B 900 MET cc_start: 0.8956 (mtp) cc_final: 0.8740 (mtm) REVERT: B 1072 GLU cc_start: 0.8681 (pm20) cc_final: 0.8287 (pm20) outliers start: 37 outliers final: 18 residues processed: 199 average time/residue: 0.1357 time to fit residues: 44.7910 Evaluate side-chains 185 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 646 ARG Chi-restraints excluded: chain C residue 649 CYS 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 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 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 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: 1.9990 chunk 83 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 0.0970 chunk 168 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 506 GLN A 207 HIS A 505 HIS A1005 GLN B 134 GLN B 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.092650 restraints weight = 35575.985| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.83 r_work: 0.2905 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26265 Z= 0.176 Angle : 0.600 11.572 35859 Z= 0.300 Chirality : 0.046 0.339 4167 Planarity : 0.004 0.053 4563 Dihedral : 5.115 56.425 4436 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.77 % Allowed : 10.68 % 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 aren not related in a simple way. whole: -1.14 (0.15), residues: 3159 helix: 0.90 (0.22), residues: 612 sheet: 0.67 (0.20), residues: 654 loop : -1.98 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.036 0.001 TYR C 495 PHE 0.021 0.002 PHE B 906 TRP 0.012 0.002 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00436 (26178) covalent geometry : angle 0.57813 (35637) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.28009 ( 78) hydrogen bonds : bond 0.05788 ( 802) hydrogen bonds : angle 4.93314 ( 2193) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 0.96492 ( 18) link_NAG-ASN : bond 0.00512 ( 42) link_NAG-ASN : angle 2.61329 ( 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 208 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.776 Fit side-chains REVERT: C 375 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: C 495 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6272 (t80) REVERT: C 1072 GLU cc_start: 0.8714 (pm20) cc_final: 0.8436 (pm20) REVERT: A 134 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: A 212 LEU cc_start: 0.4409 (OUTLIER) cc_final: 0.3909 (tp) REVERT: A 574 ASP cc_start: 0.8596 (t0) cc_final: 0.8146 (t0) REVERT: A 1138 TYR cc_start: 0.7426 (m-80) cc_final: 0.7012 (t80) REVERT: B 212 LEU cc_start: 0.4384 (OUTLIER) cc_final: 0.4063 (tp) REVERT: B 375 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 495 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.6122 (t80) REVERT: B 755 GLN cc_start: 0.8217 (mt0) cc_final: 0.8007 (mt0) REVERT: B 900 MET cc_start: 0.8937 (mtp) cc_final: 0.8727 (mtm) REVERT: B 1072 GLU cc_start: 0.8711 (pm20) cc_final: 0.8271 (pm20) outliers start: 49 outliers final: 30 residues processed: 193 average time/residue: 0.1363 time to fit residues: 44.1074 Evaluate side-chains 192 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 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 317 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 554 GLU 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 878 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 211 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 214 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3508 r_free = 0.3508 target = 0.126025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.094218 restraints weight = 35635.702| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.83 r_work: 0.2933 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1234 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= 0.118 Angle : 0.552 11.228 35859 Z= 0.275 Chirality : 0.045 0.330 4167 Planarity : 0.004 0.052 4563 Dihedral : 4.925 56.630 4436 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.52 % Allowed : 12.19 % Favored : 86.29 % 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 aren not related in a simple way. whole: -1.03 (0.15), residues: 3159 helix: 1.01 (0.23), residues: 615 sheet: 0.71 (0.21), residues: 654 loop : -1.91 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 509 TYR 0.026 0.001 TYR C 495 PHE 0.011 0.001 PHE B 906 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (26178) covalent geometry : angle 0.53021 (35637) SS BOND : bond 0.00214 ( 39) SS BOND : angle 0.97811 ( 78) hydrogen bonds : bond 0.04945 ( 802) hydrogen bonds : angle 4.80054 ( 2193) link_BETA1-4 : bond 0.00426 ( 6) link_BETA1-4 : angle 0.94432 ( 18) link_NAG-ASN : bond 0.00504 ( 42) link_NAG-ASN : angle 2.53321 ( 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 208 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.689 Fit side-chains REVERT: C 375 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: C 495 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.6187 (t80) REVERT: C 646 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7967 (mpp80) REVERT: C 1072 GLU cc_start: 0.8701 (pm20) cc_final: 0.8463 (pm20) REVERT: A 134 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: A 212 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.3781 (tp) REVERT: A 574 ASP cc_start: 0.8584 (t0) cc_final: 0.8133 (t0) REVERT: A 1138 TYR cc_start: 0.7435 (m-80) cc_final: 0.7017 (t80) REVERT: B 177 MET cc_start: 0.4525 (mmt) cc_final: 0.4174 (mmt) REVERT: B 212 LEU cc_start: 0.4347 (OUTLIER) cc_final: 0.4046 (tp) REVERT: B 375 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: B 495 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.5986 (t80) REVERT: B 574 ASP cc_start: 0.8584 (t0) cc_final: 0.8373 (t0) REVERT: B 649 CYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 755 GLN cc_start: 0.8228 (mt0) cc_final: 0.8017 (mt0) REVERT: B 900 MET cc_start: 0.8917 (mtp) cc_final: 0.8714 (mtm) REVERT: B 1072 GLU cc_start: 0.8686 (pm20) cc_final: 0.8268 (pm20) outliers start: 42 outliers final: 27 residues processed: 198 average time/residue: 0.1366 time to fit residues: 45.3336 Evaluate side-chains 193 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 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=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: 0.1980 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: 0.3980 chunk 106 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1005 GLN B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092580 restraints weight = 35628.308| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.83 r_work: 0.2900 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26265 Z= 0.168 Angle : 0.590 11.059 35859 Z= 0.295 Chirality : 0.046 0.329 4167 Planarity : 0.004 0.051 4563 Dihedral : 5.018 56.368 4436 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.62 % Allowed : 12.88 % Favored : 85.50 % 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 aren not related in a simple way. whole: -1.13 (0.15), residues: 3159 helix: 0.94 (0.22), residues: 612 sheet: 0.65 (0.20), residues: 654 loop : -1.97 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.036 0.001 TYR C 495 PHE 0.017 0.001 PHE C 86 TRP 0.012 0.002 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00412 (26178) covalent geometry : angle 0.56935 (35637) SS BOND : bond 0.00278 ( 39) SS BOND : angle 1.21157 ( 78) hydrogen bonds : bond 0.05671 ( 802) hydrogen bonds : angle 4.88594 ( 2193) link_BETA1-4 : bond 0.00452 ( 6) link_BETA1-4 : angle 0.97009 ( 18) link_NAG-ASN : bond 0.00498 ( 42) link_NAG-ASN : angle 2.53811 ( 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 204 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.720 Fit side-chains REVERT: C 375 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: C 495 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.6400 (t80) REVERT: C 1072 GLU cc_start: 0.8700 (pm20) cc_final: 0.8437 (pm20) REVERT: A 134 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6482 (tm-30) REVERT: A 212 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.3939 (tp) REVERT: A 574 ASP cc_start: 0.8610 (t0) cc_final: 0.8141 (t0) REVERT: A 1138 TYR cc_start: 0.7451 (m-80) cc_final: 0.7022 (t80) REVERT: B 177 MET cc_start: 0.4526 (mmt) cc_final: 0.4186 (mmt) REVERT: B 212 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.4091 (tp) REVERT: B 375 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: B 495 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.5876 (t80) REVERT: B 574 ASP cc_start: 0.8642 (t0) cc_final: 0.8429 (t0) REVERT: B 755 GLN cc_start: 0.8241 (mt0) cc_final: 0.8030 (mt0) REVERT: B 900 MET cc_start: 0.8931 (mtp) cc_final: 0.8721 (mtm) REVERT: B 1072 GLU cc_start: 0.8713 (pm20) cc_final: 0.8299 (pm20) outliers start: 45 outliers final: 30 residues processed: 194 average time/residue: 0.1327 time to fit residues: 42.9190 Evaluate side-chains 193 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU 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 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 705 VAL 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 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=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: 3.9990 chunk 306 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 206 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 109 optimal weight: 0.0980 chunk 283 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS 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 = 0.3489 r_free = 0.3489 target = 0.124553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.092832 restraints weight = 35631.940| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.82 r_work: 0.2907 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26265 Z= 0.148 Angle : 0.579 10.900 35859 Z= 0.288 Chirality : 0.045 0.324 4167 Planarity : 0.004 0.050 4563 Dihedral : 4.992 56.479 4436 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.66 % Allowed : 13.42 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.15), residues: 3159 helix: 0.94 (0.23), residues: 615 sheet: 0.57 (0.20), residues: 684 loop : -2.00 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.032 0.001 TYR C 495 PHE 0.014 0.001 PHE C 86 TRP 0.012 0.002 TRP C 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00359 (26178) covalent geometry : angle 0.55839 (35637) SS BOND : bond 0.00241 ( 39) SS BOND : angle 1.13424 ( 78) hydrogen bonds : bond 0.05408 ( 802) hydrogen bonds : angle 4.86021 ( 2193) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 0.96002 ( 18) link_NAG-ASN : bond 0.00487 ( 42) link_NAG-ASN : angle 2.51026 ( 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 210 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.681 Fit side-chains REVERT: C 375 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: C 495 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6382 (t80) REVERT: C 646 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7977 (mpp80) REVERT: C 787 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: C 1072 GLU cc_start: 0.8701 (pm20) cc_final: 0.8456 (pm20) REVERT: C 1138 TYR cc_start: 0.7299 (t80) cc_final: 0.7019 (t80) REVERT: A 134 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: A 212 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.3920 (tp) REVERT: A 433 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8585 (t) REVERT: A 574 ASP cc_start: 0.8599 (t0) cc_final: 0.8130 (t0) REVERT: A 1138 TYR cc_start: 0.7496 (m-80) cc_final: 0.7114 (t80) REVERT: B 177 MET cc_start: 0.4664 (mmt) cc_final: 0.4346 (mmt) REVERT: B 212 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.4103 (tp) REVERT: B 375 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: B 495 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.5808 (t80) REVERT: B 574 ASP cc_start: 0.8667 (t0) cc_final: 0.8444 (t0) REVERT: B 755 GLN cc_start: 0.8237 (mt0) cc_final: 0.8023 (mt0) REVERT: B 900 MET cc_start: 0.8914 (mtp) cc_final: 0.8701 (mtm) REVERT: B 1072 GLU cc_start: 0.8694 (pm20) cc_final: 0.8278 (pm20) outliers start: 46 outliers final: 31 residues processed: 199 average time/residue: 0.1358 time to fit residues: 45.3982 Evaluate side-chains 201 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 433 VAL 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 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 731 MET 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: 0.6980 chunk 159 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 187 optimal weight: 0.0570 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS A 207 HIS A1005 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 = 0.3522 r_free = 0.3522 target = 0.127186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.095504 restraints weight = 35524.266| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.83 r_work: 0.2951 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26265 Z= 0.100 Angle : 0.536 10.495 35859 Z= 0.265 Chirality : 0.044 0.317 4167 Planarity : 0.004 0.049 4563 Dihedral : 4.740 56.815 4436 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.26 % Allowed : 13.89 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.15), residues: 3159 helix: 1.08 (0.23), residues: 621 sheet: 0.52 (0.20), residues: 654 loop : -1.82 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 214 TYR 0.021 0.001 TYR C 495 PHE 0.012 0.001 PHE C 135 TRP 0.013 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00221 (26178) covalent geometry : angle 0.51659 (35637) SS BOND : bond 0.00146 ( 39) SS BOND : angle 0.83245 ( 78) hydrogen bonds : bond 0.04405 ( 802) hydrogen bonds : angle 4.66651 ( 2193) link_BETA1-4 : bond 0.00419 ( 6) link_BETA1-4 : angle 0.94172 ( 18) link_NAG-ASN : bond 0.00492 ( 42) link_NAG-ASN : angle 2.38175 ( 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 208 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 1.006 Fit side-chains REVERT: C 134 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6647 (tm-30) REVERT: C 375 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: C 495 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6122 (t80) REVERT: C 1072 GLU cc_start: 0.8696 (pm20) cc_final: 0.8468 (pm20) REVERT: C 1138 TYR cc_start: 0.7324 (t80) cc_final: 0.7069 (t80) REVERT: A 134 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: A 212 LEU cc_start: 0.4149 (OUTLIER) cc_final: 0.3772 (tp) REVERT: A 574 ASP cc_start: 0.8528 (t0) cc_final: 0.8024 (t0) REVERT: A 1138 TYR cc_start: 0.7503 (m-80) cc_final: 0.7115 (t80) REVERT: B 177 MET cc_start: 0.4741 (mmt) cc_final: 0.4433 (mmt) REVERT: B 212 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.4091 (tp) REVERT: B 375 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: B 495 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.5895 (t80) REVERT: B 574 ASP cc_start: 0.8719 (t0) cc_final: 0.8489 (t0) REVERT: B 649 CYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 755 GLN cc_start: 0.8223 (mt0) cc_final: 0.8015 (mt0) REVERT: B 1072 GLU cc_start: 0.8668 (pm20) cc_final: 0.8312 (pm20) outliers start: 35 outliers final: 20 residues processed: 200 average time/residue: 0.1399 time to fit residues: 47.4628 Evaluate side-chains 192 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 705 VAL 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 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 243 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 246 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS A 207 HIS A1005 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 = 0.3542 r_free = 0.3542 target = 0.128833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096858 restraints weight = 35601.415| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.93 r_work: 0.2956 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26265 Z= 0.098 Angle : 0.537 11.441 35859 Z= 0.264 Chirality : 0.044 0.317 4167 Planarity : 0.004 0.049 4563 Dihedral : 4.635 56.448 4436 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.23 % Allowed : 14.00 % Favored : 84.78 % 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 aren not related in a simple way. whole: -0.93 (0.15), residues: 3159 helix: 1.13 (0.23), residues: 621 sheet: 0.52 (0.20), residues: 657 loop : -1.75 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 815 TYR 0.021 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 covalent geometry : bond 0.00215 (26178) covalent geometry : angle 0.51892 (35637) SS BOND : bond 0.00139 ( 39) SS BOND : angle 0.85571 ( 78) hydrogen bonds : bond 0.04273 ( 802) hydrogen bonds : angle 4.59632 ( 2193) link_BETA1-4 : bond 0.00434 ( 6) link_BETA1-4 : angle 0.95105 ( 18) link_NAG-ASN : bond 0.00480 ( 42) link_NAG-ASN : angle 2.29226 ( 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 206 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.998 Fit side-chains REVERT: C 134 GLN cc_start: 0.6829 (tm-30) cc_final: 0.6600 (tm-30) REVERT: C 375 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: C 495 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.5933 (t80) REVERT: C 645 THR cc_start: 0.8553 (m) cc_final: 0.8327 (p) REVERT: C 787 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: C 1138 TYR cc_start: 0.7308 (t80) cc_final: 0.7057 (t80) REVERT: A 134 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6338 (tm-30) REVERT: A 212 LEU cc_start: 0.4070 (OUTLIER) cc_final: 0.3706 (tp) REVERT: A 529 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7428 (mmtp) REVERT: A 574 ASP cc_start: 0.8482 (t0) cc_final: 0.7961 (t0) REVERT: A 1138 TYR cc_start: 0.7515 (m-80) cc_final: 0.7056 (t80) REVERT: B 134 GLN cc_start: 0.7062 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 177 MET cc_start: 0.4708 (mmt) cc_final: 0.4392 (mmt) REVERT: B 212 LEU cc_start: 0.4454 (OUTLIER) cc_final: 0.4046 (tp) REVERT: B 375 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: B 495 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.5893 (t80) REVERT: B 574 ASP cc_start: 0.8694 (t0) cc_final: 0.8445 (t0) REVERT: B 649 CYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 755 GLN cc_start: 0.8192 (mt0) cc_final: 0.7988 (mt0) REVERT: B 1072 GLU cc_start: 0.8702 (pm20) cc_final: 0.8324 (pm20) outliers start: 34 outliers final: 22 residues processed: 197 average time/residue: 0.1514 time to fit residues: 49.7875 Evaluate side-chains 197 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 787 GLN 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 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 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: 0.9990 chunk 178 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 130 optimal weight: 0.0770 chunk 176 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 159 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 316 optimal weight: 0.6980 chunk 233 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3541 r_free = 0.3541 target = 0.128890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.096877 restraints weight = 35506.543| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.93 r_work: 0.2967 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1541 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= 0.094 Angle : 0.528 9.892 35859 Z= 0.260 Chirality : 0.044 0.314 4167 Planarity : 0.004 0.048 4563 Dihedral : 4.529 56.518 4436 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.19 % Allowed : 14.07 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 3159 helix: 1.20 (0.23), residues: 621 sheet: 0.51 (0.20), residues: 663 loop : -1.70 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.020 0.001 TYR C 495 PHE 0.011 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 covalent geometry : bond 0.00204 (26178) covalent geometry : angle 0.51092 (35637) SS BOND : bond 0.00155 ( 39) SS BOND : angle 0.84180 ( 78) hydrogen bonds : bond 0.04045 ( 802) hydrogen bonds : angle 4.52512 ( 2193) link_BETA1-4 : bond 0.00416 ( 6) link_BETA1-4 : angle 0.93369 ( 18) link_NAG-ASN : bond 0.00474 ( 42) link_NAG-ASN : angle 2.21978 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4262.89 seconds wall clock time: 74 minutes 11.11 seconds (4451.11 seconds total)