Starting phenix.real_space_refine on Sun Oct 12 13:54:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iot_35623/10_2025/8iot_35623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iot_35623/10_2025/8iot_35623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iot_35623/10_2025/8iot_35623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iot_35623/10_2025/8iot_35623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iot_35623/10_2025/8iot_35623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iot_35623/10_2025/8iot_35623.map" } resolution = 2.51 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= 0.015 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 108 5.16 5 C 15714 2.51 5 N 4041 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24642 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7990 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 53, 'TRANS': 967} Chain breaks: 7 Chain: "B" Number of atoms: 7990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7990 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 53, 'TRANS': 967} Chain breaks: 7 Chain: "C" Number of atoms: 7990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7990 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 53, 'TRANS': 967} Chain breaks: 7 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: "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 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 Time building chain proxies: 6.31, per 1000 atoms: 0.26 Number of scatterers: 24642 At special positions: 0 Unit cell: (138.69, 137.685, 167.835, 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 108 16.00 O 4779 8.00 N 4041 7.00 C 15714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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 538 " - pdb=" SG CYS A 590 " 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 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=2.04 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 538 " - pdb=" SG CYS B 590 " 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.03 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 538 " - pdb=" SG CYS C 590 " 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 C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG 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 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 343 " " 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 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 343 " " 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 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 801 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 42 sheets defined 24.0% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.511A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.814A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.831A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.792A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.121A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.548A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.914A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.512A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.815A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.831A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.792A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.122A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.547A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.915A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.511A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.814A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.831A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.793A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.122A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.548A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.914A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 5.973A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.749A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.612A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.308A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.749A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.016A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.050A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.834A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.455A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 25 through 28 removed outlier: 5.973A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.749A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.612A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.308A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.015A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.050A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.834A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.462A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 28 removed outlier: 5.973A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.012A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.612A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.307A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.015A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.049A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.835A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.558A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 934 hydrogen bonds defined for protein. 2559 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: 5.93 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7747 1.34 - 1.46: 6250 1.46 - 1.59: 11068 1.59 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 25200 Sorted by residual: bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 25195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 33893 2.36 - 4.71: 361 4.71 - 7.07: 21 7.07 - 9.43: 6 9.43 - 11.79: 3 Bond angle restraints: 34284 Sorted by residual: angle pdb=" C VAL A 656 " pdb=" N ASN A 657 " pdb=" CA ASN A 657 " ideal model delta sigma weight residual 120.38 128.09 -7.71 1.46e+00 4.69e-01 2.79e+01 angle pdb=" C VAL B 656 " pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.46e+00 4.69e-01 2.77e+01 angle pdb=" C VAL C 656 " pdb=" N ASN C 657 " pdb=" CA ASN C 657 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.46e+00 4.69e-01 2.77e+01 angle pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " pdb=" C5 NAG C1307 " ideal model delta sigma weight residual 113.21 125.00 -11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " pdb=" C5 NAG B1307 " ideal model delta sigma weight residual 113.21 124.95 -11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 34279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 14630 17.44 - 34.88: 846 34.88 - 52.32: 121 52.32 - 69.76: 42 69.76 - 87.20: 15 Dihedral angle restraints: 15654 sinusoidal: 6729 harmonic: 8925 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.98 46.98 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.95 46.95 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 15651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3923 0.112 - 0.223: 102 0.223 - 0.335: 1 0.335 - 0.446: 3 0.446 - 0.558: 3 Chirality restraints: 4032 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.72e+00 ... (remaining 4029 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " 0.010 2.00e-02 2.50e+03 5.57e-02 3.88e+01 pdb=" CG ASN C 657 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " -0.059 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.011 2.00e-02 2.50e+03 5.57e-02 3.87e+01 pdb=" CG ASN B 657 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.059 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.010 2.00e-02 2.50e+03 5.55e-02 3.85e+01 pdb=" CG ASN A 657 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.059 2.00e-02 2.50e+03 pdb=" C1 NAG A1307 " 0.054 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 744 2.72 - 3.26: 23526 3.26 - 3.81: 36985 3.81 - 4.35: 46103 4.35 - 4.90: 81084 Nonbonded interactions: 188442 Sorted by model distance: nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.169 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.169 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.169 3.040 nonbonded pdb=" O PRO B 230 " pdb=" NH1 ARG C 357 " model vdw 2.200 3.120 nonbonded pdb=" O PRO A 230 " pdb=" NH1 ARG B 357 " model vdw 2.206 3.120 ... (remaining 188437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.080 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 25287 Z= 0.172 Angle : 0.649 17.706 34506 Z= 0.315 Chirality : 0.049 0.558 4032 Planarity : 0.004 0.039 4362 Dihedral : 11.070 87.200 9789 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.21 (0.15), residues: 3015 helix: 2.59 (0.22), residues: 609 sheet: 0.87 (0.20), residues: 669 loop : -1.13 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.016 0.001 TYR A 655 PHE 0.020 0.001 PHE C 906 TRP 0.004 0.001 TRP A 64 HIS 0.002 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00337 (25200) covalent geometry : angle 0.56644 (34284) SS BOND : bond 0.00249 ( 39) SS BOND : angle 0.76252 ( 78) hydrogen bonds : bond 0.13696 ( 934) hydrogen bonds : angle 6.13711 ( 2559) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 0.82407 ( 18) link_NAG-ASN : bond 0.01013 ( 42) link_NAG-ASN : angle 5.24774 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7672 (p90) cc_final: 0.7417 (p90) REVERT: A 160 TYR cc_start: 0.8098 (p90) cc_final: 0.7818 (p90) REVERT: A 902 MET cc_start: 0.9289 (tpt) cc_final: 0.9039 (tpt) REVERT: A 955 ASN cc_start: 0.8130 (m-40) cc_final: 0.7915 (t0) REVERT: A 987 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7554 (Cg_exo) REVERT: B 140 PHE cc_start: 0.7659 (p90) cc_final: 0.7401 (p90) REVERT: B 160 TYR cc_start: 0.8226 (p90) cc_final: 0.7939 (p90) REVERT: B 955 ASN cc_start: 0.8126 (m-40) cc_final: 0.7894 (t0) REVERT: B 987 PRO cc_start: 0.7942 (Cg_endo) cc_final: 0.7367 (Cg_exo) REVERT: C 140 PHE cc_start: 0.7582 (p90) cc_final: 0.7230 (p90) REVERT: C 160 TYR cc_start: 0.8241 (p90) cc_final: 0.7963 (p90) REVERT: C 560 LEU cc_start: 0.8913 (mt) cc_final: 0.8618 (mp) REVERT: C 955 ASN cc_start: 0.8113 (m-40) cc_final: 0.7880 (t0) REVERT: C 987 PRO cc_start: 0.8086 (Cg_endo) cc_final: 0.7663 (Cg_exo) outliers start: 0 outliers final: 2 residues processed: 337 average time/residue: 0.4572 time to fit residues: 187.6326 Evaluate side-chains 193 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain C residue 368 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A 448 ASN B 207 HIS B 339 HIS B 394 ASN B 448 ASN C 339 HIS C 360 ASN C 755 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.133661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078808 restraints weight = 43209.771| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.04 r_work: 0.2894 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25287 Z= 0.120 Angle : 0.613 11.760 34506 Z= 0.302 Chirality : 0.046 0.374 4032 Planarity : 0.004 0.057 4362 Dihedral : 7.482 65.170 4291 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.34 % Allowed : 6.34 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3015 helix: 2.31 (0.21), residues: 666 sheet: 0.98 (0.20), residues: 672 loop : -1.04 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.025 0.001 TYR B 453 PHE 0.026 0.001 PHE A 429 TRP 0.020 0.002 TRP B 436 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00261 (25200) covalent geometry : angle 0.57075 (34284) SS BOND : bond 0.00227 ( 39) SS BOND : angle 0.97097 ( 78) hydrogen bonds : bond 0.04686 ( 934) hydrogen bonds : angle 4.98968 ( 2559) link_BETA1-4 : bond 0.00260 ( 6) link_BETA1-4 : angle 0.89222 ( 18) link_NAG-ASN : bond 0.00508 ( 42) link_NAG-ASN : angle 3.67633 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7417 (p90) cc_final: 0.7056 (p90) REVERT: A 160 TYR cc_start: 0.8248 (p90) cc_final: 0.7796 (p90) REVERT: A 168 PHE cc_start: 0.7715 (t80) cc_final: 0.7338 (t80) REVERT: A 339 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8256 (t70) REVERT: A 453 TYR cc_start: 0.8140 (p90) cc_final: 0.7370 (p90) REVERT: A 902 MET cc_start: 0.9328 (tpt) cc_final: 0.9038 (tpt) REVERT: A 955 ASN cc_start: 0.7777 (m-40) cc_final: 0.7423 (t0) REVERT: A 1038 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8998 (mmtp) REVERT: B 140 PHE cc_start: 0.7540 (p90) cc_final: 0.7314 (p90) REVERT: B 160 TYR cc_start: 0.8398 (p90) cc_final: 0.7776 (p90) REVERT: B 339 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8226 (t70) REVERT: B 421 TYR cc_start: 0.8615 (m-10) cc_final: 0.8238 (m-80) REVERT: B 453 TYR cc_start: 0.8128 (p90) cc_final: 0.7381 (p90) REVERT: B 753 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8290 (tp) REVERT: B 955 ASN cc_start: 0.7756 (m-40) cc_final: 0.7336 (t0) REVERT: C 140 PHE cc_start: 0.7518 (p90) cc_final: 0.7073 (p90) REVERT: C 160 TYR cc_start: 0.8286 (p90) cc_final: 0.7716 (p90) REVERT: C 339 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8403 (t70) REVERT: C 560 LEU cc_start: 0.8884 (mt) cc_final: 0.8512 (mp) REVERT: C 955 ASN cc_start: 0.7704 (m-40) cc_final: 0.7346 (t0) outliers start: 36 outliers final: 12 residues processed: 220 average time/residue: 0.4458 time to fit residues: 120.7262 Evaluate side-chains 191 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 148 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 339 HIS A 755 GLN B 207 HIS B 339 HIS B 394 ASN C 207 HIS C 339 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.069363 restraints weight = 43810.055| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.11 r_work: 0.2732 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 25287 Z= 0.270 Angle : 0.716 10.269 34506 Z= 0.366 Chirality : 0.052 0.434 4032 Planarity : 0.005 0.086 4362 Dihedral : 7.325 55.818 4291 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.05 % Allowed : 7.49 % Favored : 90.45 % 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: -0.00 (0.15), residues: 3015 helix: 1.62 (0.21), residues: 690 sheet: 0.90 (0.18), residues: 741 loop : -1.25 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1107 TYR 0.025 0.002 TYR A1067 PHE 0.039 0.002 PHE C 906 TRP 0.025 0.002 TRP B 436 HIS 0.009 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00667 (25200) covalent geometry : angle 0.67864 (34284) SS BOND : bond 0.00412 ( 39) SS BOND : angle 1.66556 ( 78) hydrogen bonds : bond 0.07768 ( 934) hydrogen bonds : angle 5.33379 ( 2559) link_BETA1-4 : bond 0.00469 ( 6) link_BETA1-4 : angle 1.44549 ( 18) link_NAG-ASN : bond 0.00367 ( 42) link_NAG-ASN : angle 3.61699 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8287 (p90) cc_final: 0.7573 (p90) REVERT: A 453 TYR cc_start: 0.8216 (p90) cc_final: 0.7395 (p90) REVERT: A 753 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8311 (tp) REVERT: A 955 ASN cc_start: 0.7882 (m-40) cc_final: 0.7506 (t0) REVERT: A 1038 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9102 (mmtp) REVERT: B 140 PHE cc_start: 0.7815 (p90) cc_final: 0.7615 (p90) REVERT: B 160 TYR cc_start: 0.8342 (p90) cc_final: 0.7744 (p90) REVERT: B 176 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7912 (mm) REVERT: B 421 TYR cc_start: 0.8595 (m-10) cc_final: 0.8259 (m-80) REVERT: B 423 TYR cc_start: 0.7703 (t80) cc_final: 0.7478 (t80) REVERT: B 453 TYR cc_start: 0.8167 (p90) cc_final: 0.7394 (p90) REVERT: B 753 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8374 (tp) REVERT: B 904 TYR cc_start: 0.8149 (m-10) cc_final: 0.7729 (m-10) REVERT: B 955 ASN cc_start: 0.7875 (m-40) cc_final: 0.7440 (t0) REVERT: C 140 PHE cc_start: 0.7666 (p90) cc_final: 0.7290 (p90) REVERT: C 160 TYR cc_start: 0.8216 (p90) cc_final: 0.7696 (p90) REVERT: C 955 ASN cc_start: 0.7820 (m-40) cc_final: 0.7378 (t0) REVERT: C 1010 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8469 (tt0) outliers start: 55 outliers final: 24 residues processed: 209 average time/residue: 0.4195 time to fit residues: 108.6045 Evaluate side-chains 206 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 103 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 chunk 194 optimal weight: 0.4980 chunk 211 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 207 HIS A 339 HIS A1088 HIS B 207 HIS B 339 HIS B 394 ASN B1088 HIS C 339 HIS C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073593 restraints weight = 43443.061| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.09 r_work: 0.2821 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25287 Z= 0.109 Angle : 0.572 10.004 34506 Z= 0.288 Chirality : 0.046 0.387 4032 Planarity : 0.004 0.061 4362 Dihedral : 6.892 59.812 4291 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.38 % Allowed : 8.99 % Favored : 89.63 % 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: 0.26 (0.15), residues: 3015 helix: 2.06 (0.21), residues: 663 sheet: 1.06 (0.19), residues: 744 loop : -1.14 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.017 0.001 TYR A 453 PHE 0.021 0.001 PHE B 168 TRP 0.022 0.001 TRP B 436 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00231 (25200) covalent geometry : angle 0.53793 (34284) SS BOND : bond 0.00223 ( 39) SS BOND : angle 0.95829 ( 78) hydrogen bonds : bond 0.04944 ( 934) hydrogen bonds : angle 4.91301 ( 2559) link_BETA1-4 : bond 0.00347 ( 6) link_BETA1-4 : angle 1.04861 ( 18) link_NAG-ASN : bond 0.00415 ( 42) link_NAG-ASN : angle 3.19332 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8159 (p90) cc_final: 0.7357 (p90) REVERT: A 168 PHE cc_start: 0.7679 (t80) cc_final: 0.7461 (t80) REVERT: A 453 TYR cc_start: 0.8206 (p90) cc_final: 0.7412 (p90) REVERT: A 955 ASN cc_start: 0.7776 (m-40) cc_final: 0.7393 (t0) REVERT: A 1038 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9046 (mmtp) REVERT: B 160 TYR cc_start: 0.8254 (p90) cc_final: 0.7643 (p90) REVERT: B 176 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7728 (mm) REVERT: B 374 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 421 TYR cc_start: 0.8650 (m-10) cc_final: 0.8293 (m-80) REVERT: B 453 TYR cc_start: 0.8247 (p90) cc_final: 0.7473 (p90) REVERT: B 955 ASN cc_start: 0.7749 (m-40) cc_final: 0.7351 (t0) REVERT: C 140 PHE cc_start: 0.7777 (p90) cc_final: 0.7343 (p90) REVERT: C 160 TYR cc_start: 0.8192 (p90) cc_final: 0.7576 (p90) REVERT: C 421 TYR cc_start: 0.8431 (m-10) cc_final: 0.8005 (m-80) REVERT: C 423 TYR cc_start: 0.7884 (t80) cc_final: 0.7667 (t80) REVERT: C 955 ASN cc_start: 0.7657 (m-40) cc_final: 0.7231 (t0) outliers start: 37 outliers final: 19 residues processed: 200 average time/residue: 0.4288 time to fit residues: 106.4444 Evaluate side-chains 193 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 214 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS B 207 HIS B 339 HIS B 394 ASN C 207 HIS C 339 HIS C 394 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.128328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070364 restraints weight = 43337.466| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.10 r_work: 0.2755 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25287 Z= 0.170 Angle : 0.609 10.063 34506 Z= 0.313 Chirality : 0.048 0.410 4032 Planarity : 0.004 0.041 4362 Dihedral : 6.742 59.565 4291 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.01 % Allowed : 9.13 % Favored : 88.85 % 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: 0.17 (0.15), residues: 3015 helix: 1.86 (0.21), residues: 690 sheet: 0.97 (0.18), residues: 744 loop : -1.17 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C1107 TYR 0.020 0.001 TYR A1067 PHE 0.023 0.002 PHE C 429 TRP 0.024 0.002 TRP B 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00410 (25200) covalent geometry : angle 0.57719 (34284) SS BOND : bond 0.00256 ( 39) SS BOND : angle 1.25488 ( 78) hydrogen bonds : bond 0.06445 ( 934) hydrogen bonds : angle 5.02675 ( 2559) link_BETA1-4 : bond 0.00110 ( 6) link_BETA1-4 : angle 1.27539 ( 18) link_NAG-ASN : bond 0.00334 ( 42) link_NAG-ASN : angle 3.13761 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8127 (p90) cc_final: 0.7558 (p90) REVERT: A 213 GLU cc_start: 0.8646 (tp30) cc_final: 0.7887 (tp30) REVERT: A 955 ASN cc_start: 0.7894 (m-40) cc_final: 0.7517 (t0) REVERT: A 1038 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9087 (mmtp) REVERT: B 160 TYR cc_start: 0.8271 (p90) cc_final: 0.7684 (p90) REVERT: B 168 PHE cc_start: 0.7714 (t80) cc_final: 0.7449 (t80) REVERT: B 176 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7849 (mm) REVERT: B 421 TYR cc_start: 0.8632 (m-10) cc_final: 0.8288 (m-80) REVERT: B 955 ASN cc_start: 0.7781 (m-40) cc_final: 0.7398 (t0) REVERT: C 140 PHE cc_start: 0.7623 (p90) cc_final: 0.7252 (p90) REVERT: C 160 TYR cc_start: 0.8165 (p90) cc_final: 0.7557 (p90) REVERT: C 176 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7902 (mm) REVERT: C 421 TYR cc_start: 0.8456 (m-10) cc_final: 0.8015 (m-80) REVERT: C 955 ASN cc_start: 0.7749 (m-40) cc_final: 0.7328 (t0) outliers start: 54 outliers final: 24 residues processed: 208 average time/residue: 0.4274 time to fit residues: 110.3807 Evaluate side-chains 195 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 292 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 283 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A1002 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 339 HIS C 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.126053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.067819 restraints weight = 43648.153| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.10 r_work: 0.2706 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25287 Z= 0.254 Angle : 0.686 11.218 34506 Z= 0.356 Chirality : 0.051 0.479 4032 Planarity : 0.005 0.066 4362 Dihedral : 6.886 59.737 4291 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.13 % Allowed : 10.03 % Favored : 87.84 % 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: -0.09 (0.15), residues: 3015 helix: 1.59 (0.20), residues: 690 sheet: 0.69 (0.18), residues: 714 loop : -1.20 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1107 TYR 0.033 0.002 TYR A 453 PHE 0.018 0.002 PHE A 92 TRP 0.025 0.002 TRP B 436 HIS 0.010 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00631 (25200) covalent geometry : angle 0.65138 (34284) SS BOND : bond 0.00574 ( 39) SS BOND : angle 1.89171 ( 78) hydrogen bonds : bond 0.07751 ( 934) hydrogen bonds : angle 5.31458 ( 2559) link_BETA1-4 : bond 0.00244 ( 6) link_BETA1-4 : angle 1.54314 ( 18) link_NAG-ASN : bond 0.00415 ( 42) link_NAG-ASN : angle 3.28459 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8650 (m-80) cc_final: 0.8408 (m-80) REVERT: A 160 TYR cc_start: 0.8113 (p90) cc_final: 0.7274 (p90) REVERT: A 168 PHE cc_start: 0.7844 (t80) cc_final: 0.7621 (t80) REVERT: A 955 ASN cc_start: 0.7920 (m-40) cc_final: 0.7541 (t0) REVERT: A 1038 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9108 (mmtp) REVERT: A 1123 SER cc_start: 0.9010 (m) cc_final: 0.8663 (p) REVERT: B 160 TYR cc_start: 0.8221 (p90) cc_final: 0.7434 (p90) REVERT: B 168 PHE cc_start: 0.7653 (t80) cc_final: 0.7415 (t80) REVERT: B 175 PHE cc_start: 0.8619 (m-10) cc_final: 0.8390 (m-10) REVERT: B 176 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7505 (mm) REVERT: B 421 TYR cc_start: 0.8638 (m-10) cc_final: 0.8325 (m-80) REVERT: B 453 TYR cc_start: 0.8352 (p90) cc_final: 0.7833 (p90) REVERT: B 753 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8321 (tp) REVERT: B 955 ASN cc_start: 0.7839 (m-40) cc_final: 0.7432 (t0) REVERT: B 1107 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7760 (mpp-170) REVERT: C 140 PHE cc_start: 0.7808 (p90) cc_final: 0.7293 (p90) REVERT: C 160 TYR cc_start: 0.8233 (p90) cc_final: 0.7735 (p90) REVERT: C 421 TYR cc_start: 0.8481 (m-10) cc_final: 0.7931 (m-80) REVERT: C 426 PRO cc_start: 0.7733 (Cg_exo) cc_final: 0.7532 (Cg_endo) REVERT: C 955 ASN cc_start: 0.7792 (m-40) cc_final: 0.7356 (t0) REVERT: C 1010 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: C 1123 SER cc_start: 0.8980 (m) cc_final: 0.8643 (p) outliers start: 57 outliers final: 33 residues processed: 212 average time/residue: 0.4137 time to fit residues: 109.9763 Evaluate side-chains 199 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 0.7980 chunk 246 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A1002 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 339 HIS C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.069755 restraints weight = 43331.843| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.09 r_work: 0.2748 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25287 Z= 0.150 Angle : 0.603 11.331 34506 Z= 0.310 Chirality : 0.047 0.440 4032 Planarity : 0.004 0.040 4362 Dihedral : 6.602 58.914 4291 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.68 % Allowed : 10.74 % Favored : 87.58 % 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: 0.05 (0.15), residues: 3015 helix: 1.73 (0.21), residues: 687 sheet: 0.92 (0.18), residues: 744 loop : -1.24 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.029 0.001 TYR A 453 PHE 0.025 0.001 PHE C 429 TRP 0.026 0.001 TRP B 436 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00356 (25200) covalent geometry : angle 0.56901 (34284) SS BOND : bond 0.00525 ( 39) SS BOND : angle 1.54665 ( 78) hydrogen bonds : bond 0.06105 ( 934) hydrogen bonds : angle 5.07353 ( 2559) link_BETA1-4 : bond 0.00245 ( 6) link_BETA1-4 : angle 1.22421 ( 18) link_NAG-ASN : bond 0.00372 ( 42) link_NAG-ASN : angle 3.12953 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9143 (m-80) cc_final: 0.8769 (p90) REVERT: A 160 TYR cc_start: 0.8102 (p90) cc_final: 0.7265 (p90) REVERT: A 177 MET cc_start: 0.5531 (pmt) cc_final: 0.4975 (pp-130) REVERT: A 421 TYR cc_start: 0.8648 (m-80) cc_final: 0.8387 (m-80) REVERT: A 955 ASN cc_start: 0.7919 (m-40) cc_final: 0.7525 (t0) REVERT: A 1038 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9075 (mmtp) REVERT: A 1123 SER cc_start: 0.8965 (m) cc_final: 0.8580 (p) REVERT: B 133 PHE cc_start: 0.8551 (m-80) cc_final: 0.8341 (m-80) REVERT: B 157 PHE cc_start: 0.9195 (m-80) cc_final: 0.8798 (p90) REVERT: B 160 TYR cc_start: 0.8194 (p90) cc_final: 0.7388 (p90) REVERT: B 168 PHE cc_start: 0.7646 (t80) cc_final: 0.7378 (t80) REVERT: B 176 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7228 (mm) REVERT: B 207 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7758 (m170) REVERT: B 374 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: B 421 TYR cc_start: 0.8649 (m-10) cc_final: 0.8318 (m-80) REVERT: B 453 TYR cc_start: 0.8371 (p90) cc_final: 0.7830 (p90) REVERT: B 753 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8294 (tp) REVERT: B 955 ASN cc_start: 0.7774 (m-40) cc_final: 0.7393 (t0) REVERT: B 1107 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7639 (mpp-170) REVERT: C 140 PHE cc_start: 0.7839 (p90) cc_final: 0.7267 (p90) REVERT: C 157 PHE cc_start: 0.9175 (m-80) cc_final: 0.8796 (p90) REVERT: C 160 TYR cc_start: 0.8191 (p90) cc_final: 0.7532 (p90) REVERT: C 421 TYR cc_start: 0.8577 (m-10) cc_final: 0.8025 (m-80) REVERT: C 423 TYR cc_start: 0.7856 (t80) cc_final: 0.7596 (t80) REVERT: C 426 PRO cc_start: 0.7780 (Cg_exo) cc_final: 0.7553 (Cg_endo) REVERT: C 955 ASN cc_start: 0.7709 (m-40) cc_final: 0.7269 (t0) outliers start: 45 outliers final: 25 residues processed: 193 average time/residue: 0.4131 time to fit residues: 100.2011 Evaluate side-chains 194 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 112 optimal weight: 9.9990 chunk 296 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 288 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A1002 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 207 HIS C 339 HIS C 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070017 restraints weight = 43336.567| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.08 r_work: 0.2752 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25287 Z= 0.145 Angle : 0.596 11.198 34506 Z= 0.307 Chirality : 0.047 0.429 4032 Planarity : 0.004 0.039 4362 Dihedral : 6.485 59.658 4291 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.72 % Allowed : 11.19 % Favored : 87.10 % 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: 0.10 (0.15), residues: 3015 helix: 1.79 (0.21), residues: 687 sheet: 0.97 (0.18), residues: 729 loop : -1.21 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.033 0.001 TYR C 453 PHE 0.023 0.001 PHE C 429 TRP 0.027 0.001 TRP C 436 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00344 (25200) covalent geometry : angle 0.56458 (34284) SS BOND : bond 0.00371 ( 39) SS BOND : angle 1.34918 ( 78) hydrogen bonds : bond 0.05935 ( 934) hydrogen bonds : angle 4.97472 ( 2559) link_BETA1-4 : bond 0.00257 ( 6) link_BETA1-4 : angle 1.22415 ( 18) link_NAG-ASN : bond 0.00367 ( 42) link_NAG-ASN : angle 3.01505 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8636 (m-80) cc_final: 0.8399 (m-80) REVERT: A 157 PHE cc_start: 0.9145 (m-80) cc_final: 0.8773 (p90) REVERT: A 160 TYR cc_start: 0.8100 (p90) cc_final: 0.7302 (p90) REVERT: A 168 PHE cc_start: 0.7778 (t80) cc_final: 0.7448 (t80) REVERT: A 177 MET cc_start: 0.6058 (pmt) cc_final: 0.5723 (pp-130) REVERT: A 409 GLN cc_start: 0.8735 (mt0) cc_final: 0.8145 (tt0) REVERT: A 421 TYR cc_start: 0.8657 (m-80) cc_final: 0.8366 (m-80) REVERT: A 955 ASN cc_start: 0.7898 (m-40) cc_final: 0.7499 (t0) REVERT: A 1038 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9074 (mmtp) REVERT: B 157 PHE cc_start: 0.9189 (m-80) cc_final: 0.8795 (p90) REVERT: B 160 TYR cc_start: 0.8205 (p90) cc_final: 0.7439 (p90) REVERT: B 168 PHE cc_start: 0.7578 (t80) cc_final: 0.7352 (t80) REVERT: B 176 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7307 (mm) REVERT: B 207 HIS cc_start: 0.7948 (t-170) cc_final: 0.7742 (m170) REVERT: B 421 TYR cc_start: 0.8656 (m-10) cc_final: 0.8306 (m-80) REVERT: B 453 TYR cc_start: 0.8414 (p90) cc_final: 0.7853 (p90) REVERT: B 753 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 955 ASN cc_start: 0.7735 (m-40) cc_final: 0.7342 (t0) REVERT: B 1107 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7725 (mpp-170) REVERT: C 140 PHE cc_start: 0.7811 (p90) cc_final: 0.7289 (p90) REVERT: C 160 TYR cc_start: 0.8176 (p90) cc_final: 0.7386 (p90) REVERT: C 421 TYR cc_start: 0.8660 (m-10) cc_final: 0.8084 (m-80) REVERT: C 426 PRO cc_start: 0.7773 (Cg_exo) cc_final: 0.7550 (Cg_endo) REVERT: C 955 ASN cc_start: 0.7693 (m-40) cc_final: 0.7270 (t0) REVERT: C 995 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7280 (mtt-85) outliers start: 46 outliers final: 28 residues processed: 201 average time/residue: 0.4030 time to fit residues: 101.7656 Evaluate side-chains 198 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 5 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 281 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 181 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A1002 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 207 HIS C 339 HIS C 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069014 restraints weight = 43426.663| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.09 r_work: 0.2735 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25287 Z= 0.173 Angle : 0.622 11.275 34506 Z= 0.320 Chirality : 0.048 0.452 4032 Planarity : 0.004 0.041 4362 Dihedral : 6.536 59.435 4291 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.79 % Allowed : 11.26 % Favored : 86.95 % 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: 0.03 (0.15), residues: 3015 helix: 1.70 (0.20), residues: 690 sheet: 0.92 (0.18), residues: 729 loop : -1.24 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.030 0.002 TYR C 453 PHE 0.037 0.002 PHE B 429 TRP 0.027 0.002 TRP B 436 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00420 (25200) covalent geometry : angle 0.59077 (34284) SS BOND : bond 0.00335 ( 39) SS BOND : angle 1.42390 ( 78) hydrogen bonds : bond 0.06527 ( 934) hydrogen bonds : angle 5.06469 ( 2559) link_BETA1-4 : bond 0.00213 ( 6) link_BETA1-4 : angle 1.29095 ( 18) link_NAG-ASN : bond 0.00375 ( 42) link_NAG-ASN : angle 3.06568 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8544 (m-80) cc_final: 0.8329 (m-80) REVERT: A 157 PHE cc_start: 0.9146 (m-80) cc_final: 0.8779 (p90) REVERT: A 160 TYR cc_start: 0.8105 (p90) cc_final: 0.7296 (p90) REVERT: A 168 PHE cc_start: 0.7926 (t80) cc_final: 0.7714 (t80) REVERT: A 176 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7397 (mm) REVERT: A 207 HIS cc_start: 0.8421 (t-170) cc_final: 0.7721 (m170) REVERT: A 409 GLN cc_start: 0.8777 (mt0) cc_final: 0.8168 (tt0) REVERT: A 421 TYR cc_start: 0.8643 (m-80) cc_final: 0.8327 (m-80) REVERT: A 955 ASN cc_start: 0.7935 (m-40) cc_final: 0.7547 (t0) REVERT: A 1038 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9084 (mmtp) REVERT: A 1123 SER cc_start: 0.8959 (m) cc_final: 0.8585 (p) REVERT: B 157 PHE cc_start: 0.9194 (m-80) cc_final: 0.8795 (p90) REVERT: B 160 TYR cc_start: 0.8207 (p90) cc_final: 0.7429 (p90) REVERT: B 176 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7275 (mm) REVERT: B 207 HIS cc_start: 0.8068 (t-170) cc_final: 0.7779 (m170) REVERT: B 421 TYR cc_start: 0.8687 (m-10) cc_final: 0.8371 (m-80) REVERT: B 453 TYR cc_start: 0.8430 (p90) cc_final: 0.7874 (p90) REVERT: B 753 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8314 (tp) REVERT: B 955 ASN cc_start: 0.7800 (m-40) cc_final: 0.7417 (t0) REVERT: B 1107 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7651 (mpp-170) REVERT: C 140 PHE cc_start: 0.7822 (p90) cc_final: 0.7272 (p90) REVERT: C 160 TYR cc_start: 0.8185 (p90) cc_final: 0.7528 (p90) REVERT: C 198 ASP cc_start: 0.8006 (p0) cc_final: 0.7788 (p0) REVERT: C 421 TYR cc_start: 0.8718 (m-10) cc_final: 0.8166 (m-80) REVERT: C 423 TYR cc_start: 0.8040 (t80) cc_final: 0.7720 (t80) REVERT: C 426 PRO cc_start: 0.7808 (Cg_exo) cc_final: 0.7607 (Cg_endo) REVERT: C 955 ASN cc_start: 0.7715 (m-40) cc_final: 0.7291 (t0) REVERT: C 995 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7378 (mtt-85) outliers start: 48 outliers final: 30 residues processed: 195 average time/residue: 0.3835 time to fit residues: 94.2434 Evaluate side-chains 197 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 256 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 282 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 238 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A1002 GLN B 339 HIS B 394 ASN B1002 GLN C 339 HIS C 394 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.070789 restraints weight = 43305.720| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.08 r_work: 0.2772 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25287 Z= 0.124 Angle : 0.585 11.125 34506 Z= 0.299 Chirality : 0.047 0.422 4032 Planarity : 0.004 0.040 4362 Dihedral : 6.410 59.858 4291 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.60 % Allowed : 11.56 % Favored : 86.84 % 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: 0.17 (0.15), residues: 3015 helix: 1.86 (0.21), residues: 687 sheet: 1.04 (0.19), residues: 729 loop : -1.18 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.030 0.001 TYR C 453 PHE 0.023 0.001 PHE C 429 TRP 0.028 0.001 TRP B 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00282 (25200) covalent geometry : angle 0.55616 (34284) SS BOND : bond 0.00324 ( 39) SS BOND : angle 1.14813 ( 78) hydrogen bonds : bond 0.05426 ( 934) hydrogen bonds : angle 4.88931 ( 2559) link_BETA1-4 : bond 0.00289 ( 6) link_BETA1-4 : angle 1.12689 ( 18) link_NAG-ASN : bond 0.00374 ( 42) link_NAG-ASN : angle 2.94284 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8534 (m-80) cc_final: 0.8316 (m-80) REVERT: A 157 PHE cc_start: 0.9181 (m-80) cc_final: 0.8795 (p90) REVERT: A 160 TYR cc_start: 0.8087 (p90) cc_final: 0.7279 (p90) REVERT: A 168 PHE cc_start: 0.8015 (t80) cc_final: 0.7690 (t80) REVERT: A 409 GLN cc_start: 0.8784 (mt0) cc_final: 0.8189 (tt0) REVERT: A 421 TYR cc_start: 0.8662 (m-80) cc_final: 0.8358 (m-80) REVERT: A 955 ASN cc_start: 0.7878 (m-40) cc_final: 0.7484 (t0) REVERT: A 987 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8237 (Cg_endo) REVERT: A 1038 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9081 (mmtp) REVERT: B 157 PHE cc_start: 0.9167 (m-80) cc_final: 0.8773 (p90) REVERT: B 160 TYR cc_start: 0.8247 (p90) cc_final: 0.7486 (p90) REVERT: B 176 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7299 (mm) REVERT: B 207 HIS cc_start: 0.8031 (t-170) cc_final: 0.7749 (m170) REVERT: B 421 TYR cc_start: 0.8697 (m-10) cc_final: 0.8377 (m-80) REVERT: B 453 TYR cc_start: 0.8465 (p90) cc_final: 0.7946 (p90) REVERT: B 753 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8316 (tp) REVERT: B 955 ASN cc_start: 0.7716 (m-40) cc_final: 0.7329 (t0) REVERT: B 1107 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7820 (mpp-170) REVERT: C 140 PHE cc_start: 0.7819 (p90) cc_final: 0.7241 (p90) REVERT: C 157 PHE cc_start: 0.9182 (m-80) cc_final: 0.8793 (p90) REVERT: C 160 TYR cc_start: 0.8153 (p90) cc_final: 0.7446 (p90) REVERT: C 421 TYR cc_start: 0.8725 (m-10) cc_final: 0.8146 (m-80) REVERT: C 426 PRO cc_start: 0.7852 (Cg_exo) cc_final: 0.7627 (Cg_endo) REVERT: C 955 ASN cc_start: 0.7672 (m-40) cc_final: 0.7254 (t0) REVERT: C 995 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7234 (mtt-85) outliers start: 43 outliers final: 25 residues processed: 195 average time/residue: 0.4104 time to fit residues: 100.8924 Evaluate side-chains 192 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 141 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A1002 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 339 HIS C 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.127391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.069637 restraints weight = 43238.737| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.09 r_work: 0.2751 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25287 Z= 0.151 Angle : 0.605 11.136 34506 Z= 0.311 Chirality : 0.048 0.437 4032 Planarity : 0.004 0.039 4362 Dihedral : 6.423 59.939 4289 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.30 % Allowed : 12.01 % Favored : 86.69 % 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: 0.14 (0.15), residues: 3015 helix: 1.83 (0.21), residues: 690 sheet: 1.00 (0.19), residues: 729 loop : -1.19 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.029 0.001 TYR C 453 PHE 0.035 0.001 PHE B 429 TRP 0.026 0.001 TRP B 436 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (25200) covalent geometry : angle 0.57566 (34284) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.28903 ( 78) hydrogen bonds : bond 0.06054 ( 934) hydrogen bonds : angle 4.95427 ( 2559) link_BETA1-4 : bond 0.00264 ( 6) link_BETA1-4 : angle 1.20964 ( 18) link_NAG-ASN : bond 0.00363 ( 42) link_NAG-ASN : angle 2.95293 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13284.82 seconds wall clock time: 225 minutes 38.09 seconds (13538.09 seconds total)