Starting phenix.real_space_refine on Fri May 23 23:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iot_35623/05_2025/8iot_35623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iot_35623/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iot_35623/05_2025/8iot_35623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iot_35623/05_2025/8iot_35623.map" model { file = "/net/cci-nas-00/data/ceres_data/8iot_35623/05_2025/8iot_35623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iot_35623/05_2025/8iot_35623.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.41, per 1000 atoms: 0.58 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: 5.85 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.13 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: 11.19 Time building geometry restraints manager: 6.91 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: 0.00 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: 4.090 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: 1.100 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 56.280 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP A 64 HIS 0.002 0.000 HIS B 339 PHE 0.020 0.001 PHE C 906 TYR 0.016 0.001 TYR A 655 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01013 ( 42) link_NAG-ASN : angle 5.24774 ( 126) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 0.82407 ( 18) hydrogen bonds : bond 0.13696 ( 934) hydrogen bonds : angle 6.13711 ( 2559) SS BOND : bond 0.00249 ( 39) SS BOND : angle 0.76252 ( 78) covalent geometry : bond 0.00337 (25200) covalent geometry : angle 0.56644 (34284) *********************** 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 : 2.695 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: 0.7559 (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: 0.7372 (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: 0.7964 (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: 0.8931 time to fit residues: 369.5023 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 : 2.583 ------------------------------------------------------------------------------- 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 258 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.131291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073578 restraints weight = 43545.865| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.14 r_work: 0.2817 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1532 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= 0.162 Angle : 0.650 11.658 34506 Z= 0.325 Chirality : 0.048 0.400 4032 Planarity : 0.004 0.058 4362 Dihedral : 7.535 64.293 4291 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.53 % Allowed : 6.49 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3015 helix: 2.14 (0.21), residues: 669 sheet: 1.05 (0.19), residues: 735 loop : -1.16 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 436 HIS 0.007 0.001 HIS A 207 PHE 0.033 0.002 PHE C 906 TYR 0.026 0.002 TYR B 453 ARG 0.009 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 42) link_NAG-ASN : angle 3.68774 ( 126) link_BETA1-4 : bond 0.00116 ( 6) link_BETA1-4 : angle 0.98295 ( 18) hydrogen bonds : bond 0.05820 ( 934) hydrogen bonds : angle 5.09722 ( 2559) SS BOND : bond 0.00553 ( 39) SS BOND : angle 1.23291 ( 78) covalent geometry : bond 0.00381 (25200) covalent geometry : angle 0.60908 (34284) *********************** 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 239 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7476 (p90) cc_final: 0.7126 (p90) REVERT: A 160 TYR cc_start: 0.8272 (p90) cc_final: 0.7800 (p90) REVERT: A 168 PHE cc_start: 0.7692 (t80) cc_final: 0.7463 (t80) REVERT: A 339 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8265 (t70) REVERT: A 453 TYR cc_start: 0.8166 (p90) cc_final: 0.7381 (p90) REVERT: A 753 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 902 MET cc_start: 0.9303 (tpt) cc_final: 0.8953 (tpt) REVERT: A 955 ASN cc_start: 0.7785 (m-40) cc_final: 0.7408 (t0) REVERT: A 1038 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9043 (mmtp) REVERT: B 140 PHE cc_start: 0.7598 (p90) cc_final: 0.7328 (p90) REVERT: B 160 TYR cc_start: 0.8377 (p90) cc_final: 0.7766 (p90) REVERT: B 176 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7875 (mm) REVERT: B 339 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8230 (t70) REVERT: B 357 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (ttt180) REVERT: B 421 TYR cc_start: 0.8603 (m-10) cc_final: 0.8230 (m-80) REVERT: B 423 TYR cc_start: 0.7616 (t80) cc_final: 0.7407 (t80) REVERT: B 453 TYR cc_start: 0.8145 (p90) cc_final: 0.7401 (p90) REVERT: B 753 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8284 (tp) REVERT: B 904 TYR cc_start: 0.8170 (m-10) cc_final: 0.7886 (m-10) REVERT: B 955 ASN cc_start: 0.7774 (m-40) cc_final: 0.7334 (t0) REVERT: C 52 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8150 (tm-30) REVERT: C 140 PHE cc_start: 0.7517 (p90) cc_final: 0.7003 (p90) REVERT: C 160 TYR cc_start: 0.8258 (p90) cc_final: 0.7662 (p90) REVERT: C 339 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8399 (t70) REVERT: C 560 LEU cc_start: 0.8893 (mt) cc_final: 0.8499 (mp) REVERT: C 955 ASN cc_start: 0.7788 (m-40) cc_final: 0.7382 (t0) outliers start: 41 outliers final: 12 residues processed: 217 average time/residue: 0.8978 time to fit residues: 240.3268 Evaluate side-chains 192 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 2.691 ------------------------------------------------------------------------------- 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 753 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 357 ARG 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 51 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 263 optimal weight: 0.2980 chunk 200 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 755 GLN B 207 HIS B 394 ASN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075308 restraints weight = 42978.001| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.08 r_work: 0.2827 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1730 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= 0.126 Angle : 0.596 10.249 34506 Z= 0.298 Chirality : 0.046 0.373 4032 Planarity : 0.004 0.039 4362 Dihedral : 7.089 58.866 4291 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.60 % Allowed : 7.46 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3015 helix: 2.08 (0.21), residues: 669 sheet: 1.09 (0.18), residues: 738 loop : -1.15 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 436 HIS 0.007 0.001 HIS A 207 PHE 0.020 0.001 PHE C 133 TYR 0.022 0.001 TYR B 453 ARG 0.006 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 42) link_NAG-ASN : angle 3.39005 ( 126) link_BETA1-4 : bond 0.00421 ( 6) link_BETA1-4 : angle 1.12420 ( 18) hydrogen bonds : bond 0.05237 ( 934) hydrogen bonds : angle 4.95980 ( 2559) SS BOND : bond 0.00622 ( 39) SS BOND : angle 1.08530 ( 78) covalent geometry : bond 0.00282 (25200) covalent geometry : angle 0.55814 (34284) *********************** 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 223 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7628 (p90) cc_final: 0.7334 (p90) REVERT: A 160 TYR cc_start: 0.8337 (p90) cc_final: 0.7432 (p90) REVERT: A 340 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8288 (mp0) REVERT: A 453 TYR cc_start: 0.8178 (p90) cc_final: 0.7414 (p90) REVERT: A 902 MET cc_start: 0.9286 (tpt) cc_final: 0.8936 (tpt) REVERT: A 955 ASN cc_start: 0.7785 (m-40) cc_final: 0.7420 (t0) REVERT: A 1038 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9061 (mmtp) REVERT: B 160 TYR cc_start: 0.8329 (p90) cc_final: 0.7706 (p90) REVERT: B 176 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7624 (mm) REVERT: B 340 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8167 (mp0) REVERT: B 421 TYR cc_start: 0.8622 (m-10) cc_final: 0.8253 (m-80) REVERT: B 423 TYR cc_start: 0.7657 (t80) cc_final: 0.7418 (t80) REVERT: B 453 TYR cc_start: 0.8194 (p90) cc_final: 0.7419 (p90) REVERT: B 753 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8233 (tp) REVERT: B 955 ASN cc_start: 0.7754 (m-40) cc_final: 0.7350 (t0) REVERT: C 140 PHE cc_start: 0.7714 (p90) cc_final: 0.7377 (p90) REVERT: C 160 TYR cc_start: 0.8217 (p90) cc_final: 0.7626 (p90) REVERT: C 379 CYS cc_start: 0.5857 (m) cc_final: 0.5613 (m) REVERT: C 421 TYR cc_start: 0.8559 (m-10) cc_final: 0.8052 (m-80) REVERT: C 955 ASN cc_start: 0.7699 (m-40) cc_final: 0.7312 (t0) outliers start: 43 outliers final: 18 residues processed: 199 average time/residue: 0.9250 time to fit residues: 229.1739 Evaluate side-chains 193 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 HIS 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 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE 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 339 HIS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 152 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 chunk 249 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 A1088 HIS B 207 HIS B 339 HIS B 394 ASN C 207 HIS C 339 HIS C1088 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.074264 restraints weight = 43273.611| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.11 r_work: 0.2807 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25287 Z= 0.127 Angle : 0.573 9.340 34506 Z= 0.291 Chirality : 0.046 0.375 4032 Planarity : 0.004 0.037 4362 Dihedral : 6.819 59.105 4291 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.42 % Allowed : 8.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3015 helix: 2.13 (0.21), residues: 669 sheet: 1.09 (0.18), residues: 741 loop : -1.13 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 436 HIS 0.007 0.001 HIS A 207 PHE 0.026 0.001 PHE A 429 TYR 0.019 0.001 TYR B 453 ARG 0.008 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 42) link_NAG-ASN : angle 3.10603 ( 126) link_BETA1-4 : bond 0.00202 ( 6) link_BETA1-4 : angle 1.10029 ( 18) hydrogen bonds : bond 0.05329 ( 934) hydrogen bonds : angle 4.86890 ( 2559) SS BOND : bond 0.00256 ( 39) SS BOND : angle 1.03486 ( 78) covalent geometry : bond 0.00292 (25200) covalent geometry : angle 0.54050 (34284) *********************** 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 219 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7755 (p90) cc_final: 0.7507 (p90) REVERT: A 160 TYR cc_start: 0.8188 (p90) cc_final: 0.7366 (p90) REVERT: A 453 TYR cc_start: 0.8197 (p90) cc_final: 0.7397 (p90) REVERT: A 753 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8341 (tp) REVERT: A 955 ASN cc_start: 0.7793 (m-40) cc_final: 0.7425 (t0) REVERT: A 1038 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9060 (mmtp) REVERT: B 160 TYR cc_start: 0.8271 (p90) cc_final: 0.7661 (p90) REVERT: B 421 TYR cc_start: 0.8658 (m-10) cc_final: 0.8274 (m-80) REVERT: B 423 TYR cc_start: 0.7757 (t80) cc_final: 0.7529 (t80) REVERT: B 453 TYR cc_start: 0.8247 (p90) cc_final: 0.7487 (p90) REVERT: B 753 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8188 (tp) REVERT: B 904 TYR cc_start: 0.7994 (m-10) cc_final: 0.7664 (m-10) REVERT: B 955 ASN cc_start: 0.7757 (m-40) cc_final: 0.7354 (t0) REVERT: C 140 PHE cc_start: 0.7753 (p90) cc_final: 0.7357 (p90) REVERT: C 160 TYR cc_start: 0.8185 (p90) cc_final: 0.7623 (p90) REVERT: C 955 ASN cc_start: 0.7717 (m-40) cc_final: 0.7310 (t0) outliers start: 38 outliers final: 21 residues processed: 202 average time/residue: 0.8380 time to fit residues: 213.7758 Evaluate side-chains 196 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 565 PHE Chi-restraints excluded: chain A residue 569 ILE 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 351 TYR 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 394 ASN Chi-restraints excluded: chain B residue 434 ILE 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 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 40 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 108 optimal weight: 0.0050 chunk 225 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 147 optimal weight: 0.0270 chunk 204 optimal weight: 10.0000 overall best weight: 0.7656 ------------------------------------------------------------------------------- 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 B1088 HIS 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 = 0.3941 r_free = 0.3941 target = 0.130793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073501 restraints weight = 43517.876| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.13 r_work: 0.2818 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25287 Z= 0.112 Angle : 0.550 9.359 34506 Z= 0.280 Chirality : 0.046 0.365 4032 Planarity : 0.004 0.036 4362 Dihedral : 6.533 59.345 4291 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.49 % Allowed : 9.73 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3015 helix: 2.17 (0.21), residues: 669 sheet: 1.15 (0.18), residues: 741 loop : -1.08 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 436 HIS 0.011 0.001 HIS A 207 PHE 0.021 0.001 PHE C 133 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 42) link_NAG-ASN : angle 2.95459 ( 126) link_BETA1-4 : bond 0.00268 ( 6) link_BETA1-4 : angle 1.07060 ( 18) hydrogen bonds : bond 0.04912 ( 934) hydrogen bonds : angle 4.76720 ( 2559) SS BOND : bond 0.00205 ( 39) SS BOND : angle 0.95452 ( 78) covalent geometry : bond 0.00248 (25200) covalent geometry : angle 0.51941 (34284) *********************** 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 220 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7795 (p90) cc_final: 0.7477 (p90) REVERT: A 157 PHE cc_start: 0.9168 (m-80) cc_final: 0.8791 (p90) REVERT: A 160 TYR cc_start: 0.8132 (p90) cc_final: 0.7390 (p90) REVERT: A 955 ASN cc_start: 0.7760 (m-40) cc_final: 0.7387 (t0) REVERT: A 1038 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9037 (mmtp) REVERT: B 157 PHE cc_start: 0.9177 (m-80) cc_final: 0.8791 (p90) REVERT: B 160 TYR cc_start: 0.8283 (p90) cc_final: 0.7645 (p90) REVERT: B 168 PHE cc_start: 0.7759 (t80) cc_final: 0.7511 (t80) REVERT: B 374 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: B 421 TYR cc_start: 0.8637 (m-10) cc_final: 0.8263 (m-80) REVERT: B 453 TYR cc_start: 0.8291 (p90) cc_final: 0.7558 (p90) REVERT: B 753 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8176 (tp) REVERT: B 904 TYR cc_start: 0.8068 (m-10) cc_final: 0.7665 (m-10) REVERT: B 955 ASN cc_start: 0.7706 (m-40) cc_final: 0.7305 (t0) REVERT: C 140 PHE cc_start: 0.7740 (p90) cc_final: 0.7257 (p90) REVERT: C 160 TYR cc_start: 0.8171 (p90) cc_final: 0.7619 (p90) REVERT: C 955 ASN cc_start: 0.7644 (m-40) cc_final: 0.7233 (t0) outliers start: 40 outliers final: 19 residues processed: 202 average time/residue: 0.7759 time to fit residues: 199.5418 Evaluate side-chains 190 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 2.580 ------------------------------------------------------------------------------- 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 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 351 TYR 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 434 ILE Chi-restraints excluded: chain B residue 753 LEU 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 569 ILE Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 188 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.128288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070248 restraints weight = 43248.679| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.09 r_work: 0.2752 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25287 Z= 0.166 Angle : 0.608 9.658 34506 Z= 0.315 Chirality : 0.048 0.400 4032 Planarity : 0.004 0.042 4362 Dihedral : 6.513 59.257 4291 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.60 % Allowed : 10.10 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3015 helix: 1.92 (0.21), residues: 687 sheet: 1.01 (0.19), residues: 729 loop : -1.10 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 436 HIS 0.011 0.001 HIS C 207 PHE 0.028 0.002 PHE A 429 TYR 0.030 0.001 TYR A 453 ARG 0.009 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 42) link_NAG-ASN : angle 2.95143 ( 126) link_BETA1-4 : bond 0.00097 ( 6) link_BETA1-4 : angle 1.27500 ( 18) hydrogen bonds : bond 0.06526 ( 934) hydrogen bonds : angle 5.07536 ( 2559) SS BOND : bond 0.00251 ( 39) SS BOND : angle 1.29630 ( 78) covalent geometry : bond 0.00400 (25200) covalent geometry : angle 0.57947 (34284) *********************** 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 223 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8575 (m-80) cc_final: 0.8371 (m-80) REVERT: A 140 PHE cc_start: 0.7868 (p90) cc_final: 0.7577 (p90) REVERT: A 160 TYR cc_start: 0.8117 (p90) cc_final: 0.7375 (p90) REVERT: A 168 PHE cc_start: 0.7737 (t80) cc_final: 0.7532 (t80) REVERT: A 453 TYR cc_start: 0.8214 (p90) cc_final: 0.7501 (p90) REVERT: A 955 ASN cc_start: 0.7833 (m-40) cc_final: 0.7459 (t0) REVERT: A 1038 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9088 (mmtp) REVERT: B 160 TYR cc_start: 0.8298 (p90) cc_final: 0.7640 (p90) REVERT: B 168 PHE cc_start: 0.7765 (t80) cc_final: 0.7456 (t80) REVERT: B 374 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: B 421 TYR cc_start: 0.8671 (m-10) cc_final: 0.8330 (m-80) REVERT: B 453 TYR cc_start: 0.8336 (p90) cc_final: 0.7676 (p90) REVERT: B 753 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8328 (tp) REVERT: B 955 ASN cc_start: 0.7819 (m-40) cc_final: 0.7424 (t0) REVERT: C 140 PHE cc_start: 0.7645 (p90) cc_final: 0.7240 (p90) REVERT: C 160 TYR cc_start: 0.8228 (p90) cc_final: 0.7679 (p90) REVERT: C 176 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7885 (mm) REVERT: C 955 ASN cc_start: 0.7745 (m-40) cc_final: 0.7322 (t0) outliers start: 43 outliers final: 25 residues processed: 207 average time/residue: 0.7937 time to fit residues: 208.2522 Evaluate side-chains 197 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 2.643 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE 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 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 753 LEU 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 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 257 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.127382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.069434 restraints weight = 43419.653| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.09 r_work: 0.2740 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25287 Z= 0.195 Angle : 0.626 10.388 34506 Z= 0.324 Chirality : 0.049 0.431 4032 Planarity : 0.004 0.040 4362 Dihedral : 6.585 59.705 4291 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.38 % Allowed : 10.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3015 helix: 1.81 (0.21), residues: 687 sheet: 0.96 (0.19), residues: 729 loop : -1.14 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 436 HIS 0.008 0.001 HIS C 207 PHE 0.021 0.002 PHE B 133 TYR 0.027 0.001 TYR A 453 ARG 0.008 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 42) link_NAG-ASN : angle 3.01892 ( 126) link_BETA1-4 : bond 0.00188 ( 6) link_BETA1-4 : angle 1.34326 ( 18) hydrogen bonds : bond 0.06689 ( 934) hydrogen bonds : angle 5.10701 ( 2559) SS BOND : bond 0.00525 ( 39) SS BOND : angle 1.82985 ( 78) covalent geometry : bond 0.00478 (25200) covalent geometry : angle 0.59368 (34284) *********************** 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 210 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7954 (p90) cc_final: 0.7596 (p90) REVERT: A 160 TYR cc_start: 0.8105 (p90) cc_final: 0.7343 (p90) REVERT: A 168 PHE cc_start: 0.7681 (t80) cc_final: 0.7476 (t80) REVERT: A 374 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 421 TYR cc_start: 0.8638 (m-80) cc_final: 0.8410 (m-80) REVERT: A 955 ASN cc_start: 0.7861 (m-40) cc_final: 0.7492 (t0) REVERT: A 1038 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9088 (mmtp) REVERT: A 1123 SER cc_start: 0.8953 (m) cc_final: 0.8577 (p) REVERT: B 160 TYR cc_start: 0.8264 (p90) cc_final: 0.7642 (p90) REVERT: B 168 PHE cc_start: 0.7677 (t80) cc_final: 0.7409 (t80) REVERT: B 176 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7883 (mm) REVERT: B 374 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: B 421 TYR cc_start: 0.8675 (m-10) cc_final: 0.8312 (m-80) REVERT: B 453 TYR cc_start: 0.8343 (p90) cc_final: 0.7676 (p90) REVERT: B 753 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8322 (tp) REVERT: B 955 ASN cc_start: 0.7789 (m-40) cc_final: 0.7408 (t0) REVERT: C 140 PHE cc_start: 0.7785 (p90) cc_final: 0.7283 (p90) REVERT: C 157 PHE cc_start: 0.9214 (m-80) cc_final: 0.8822 (p90) REVERT: C 160 TYR cc_start: 0.8204 (p90) cc_final: 0.7671 (p90) REVERT: C 176 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7994 (mm) REVERT: C 374 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: C 955 ASN cc_start: 0.7725 (m-40) cc_final: 0.7296 (t0) outliers start: 37 outliers final: 26 residues processed: 194 average time/residue: 0.7619 time to fit residues: 188.7193 Evaluate side-chains 197 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 2.964 ------------------------------------------------------------------------------- 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 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 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 753 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 117 LEU 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 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 129 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072854 restraints weight = 43452.659| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.10 r_work: 0.2811 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25287 Z= 0.106 Angle : 0.553 10.320 34506 Z= 0.282 Chirality : 0.045 0.388 4032 Planarity : 0.004 0.037 4362 Dihedral : 6.273 59.302 4291 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.23 % Allowed : 10.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3015 helix: 2.18 (0.21), residues: 660 sheet: 1.17 (0.19), residues: 726 loop : -1.04 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 436 HIS 0.012 0.001 HIS C 207 PHE 0.033 0.001 PHE B 429 TYR 0.028 0.001 TYR A 453 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 42) link_NAG-ASN : angle 2.82999 ( 126) link_BETA1-4 : bond 0.00359 ( 6) link_BETA1-4 : angle 1.02449 ( 18) hydrogen bonds : bond 0.04704 ( 934) hydrogen bonds : angle 4.81230 ( 2559) SS BOND : bond 0.00386 ( 39) SS BOND : angle 1.15406 ( 78) covalent geometry : bond 0.00225 (25200) covalent geometry : angle 0.52372 (34284) *********************** 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 209 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8005 (p90) cc_final: 0.7665 (p90) REVERT: A 157 PHE cc_start: 0.9170 (m-80) cc_final: 0.8758 (p90) REVERT: A 160 TYR cc_start: 0.8065 (p90) cc_final: 0.7302 (p90) REVERT: A 177 MET cc_start: 0.6109 (pmt) cc_final: 0.5824 (pp-130) REVERT: A 374 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 421 TYR cc_start: 0.8626 (m-80) cc_final: 0.8344 (m-80) REVERT: A 955 ASN cc_start: 0.7840 (m-40) cc_final: 0.7455 (t0) REVERT: A 1038 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9069 (mmtp) REVERT: B 157 PHE cc_start: 0.9167 (m-80) cc_final: 0.8779 (p90) REVERT: B 160 TYR cc_start: 0.8252 (p90) cc_final: 0.7493 (p90) REVERT: B 168 PHE cc_start: 0.7662 (t80) cc_final: 0.7441 (t80) REVERT: B 176 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7081 (mm) REVERT: B 207 HIS cc_start: 0.8183 (t-170) cc_final: 0.7685 (m170) REVERT: B 421 TYR cc_start: 0.8753 (m-10) cc_final: 0.8380 (m-80) REVERT: B 453 TYR cc_start: 0.8329 (p90) cc_final: 0.7735 (p90) REVERT: B 955 ASN cc_start: 0.7713 (m-40) cc_final: 0.7322 (t0) REVERT: C 140 PHE cc_start: 0.7731 (p90) cc_final: 0.7223 (p90) REVERT: C 157 PHE cc_start: 0.9239 (m-80) cc_final: 0.8845 (p90) REVERT: C 160 TYR cc_start: 0.8135 (p90) cc_final: 0.7493 (p90) REVERT: C 176 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7768 (mm) REVERT: C 198 ASP cc_start: 0.8062 (p0) cc_final: 0.7860 (p0) REVERT: C 421 TYR cc_start: 0.8741 (m-10) cc_final: 0.8144 (m-80) REVERT: C 423 TYR cc_start: 0.7772 (t80) cc_final: 0.7516 (t80) REVERT: C 955 ASN cc_start: 0.7650 (m-40) cc_final: 0.7245 (t0) outliers start: 33 outliers final: 20 residues processed: 191 average time/residue: 0.7197 time to fit residues: 178.1862 Evaluate side-chains 188 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 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 374 PHE 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 208 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 382 VAL 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 565 PHE Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 158 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 288 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS B 207 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.128680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.071002 restraints weight = 43481.582| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.09 r_work: 0.2772 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25287 Z= 0.136 Angle : 0.580 9.989 34506 Z= 0.298 Chirality : 0.047 0.397 4032 Planarity : 0.004 0.038 4362 Dihedral : 6.291 59.860 4291 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.30 % Allowed : 11.48 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3015 helix: 2.07 (0.21), residues: 684 sheet: 1.13 (0.19), residues: 726 loop : -1.05 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 436 HIS 0.011 0.001 HIS C 207 PHE 0.023 0.001 PHE B 133 TYR 0.033 0.001 TYR C 453 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 42) link_NAG-ASN : angle 2.80280 ( 126) link_BETA1-4 : bond 0.00211 ( 6) link_BETA1-4 : angle 1.13690 ( 18) hydrogen bonds : bond 0.05564 ( 934) hydrogen bonds : angle 4.87303 ( 2559) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.24730 ( 78) covalent geometry : bond 0.00318 (25200) covalent geometry : angle 0.55236 (34284) *********************** 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 204 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8374 (m-80) cc_final: 0.8151 (m-80) REVERT: A 140 PHE cc_start: 0.8046 (p90) cc_final: 0.7695 (p90) REVERT: A 157 PHE cc_start: 0.9159 (m-80) cc_final: 0.8752 (p90) REVERT: A 160 TYR cc_start: 0.8081 (p90) cc_final: 0.7309 (p90) REVERT: A 207 HIS cc_start: 0.8352 (t-170) cc_final: 0.7662 (m170) REVERT: A 374 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: A 421 TYR cc_start: 0.8631 (m-80) cc_final: 0.8357 (m-80) REVERT: A 955 ASN cc_start: 0.7845 (m-40) cc_final: 0.7483 (t0) REVERT: A 1038 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9073 (mmtp) REVERT: B 157 PHE cc_start: 0.9166 (m-80) cc_final: 0.8786 (p90) REVERT: B 160 TYR cc_start: 0.8238 (p90) cc_final: 0.7573 (p90) REVERT: B 168 PHE cc_start: 0.7585 (t80) cc_final: 0.7292 (t80) REVERT: B 421 TYR cc_start: 0.8747 (m-10) cc_final: 0.8377 (m-80) REVERT: B 453 TYR cc_start: 0.8337 (p90) cc_final: 0.7739 (p90) REVERT: B 955 ASN cc_start: 0.7715 (m-40) cc_final: 0.7332 (t0) REVERT: C 140 PHE cc_start: 0.7764 (p90) cc_final: 0.7240 (p90) REVERT: C 157 PHE cc_start: 0.9239 (m-80) cc_final: 0.8854 (p90) REVERT: C 160 TYR cc_start: 0.8169 (p90) cc_final: 0.7563 (p90) REVERT: C 176 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7753 (mm) REVERT: C 421 TYR cc_start: 0.8739 (m-10) cc_final: 0.8143 (m-80) REVERT: C 423 TYR cc_start: 0.7818 (t80) cc_final: 0.7568 (t80) REVERT: C 955 ASN cc_start: 0.7670 (m-40) cc_final: 0.7286 (t0) outliers start: 35 outliers final: 20 residues processed: 188 average time/residue: 0.7605 time to fit residues: 183.0097 Evaluate side-chains 186 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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 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 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 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 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 565 PHE Chi-restraints excluded: chain C residue 569 ILE 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 224 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 207 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068451 restraints weight = 43250.963| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.08 r_work: 0.2720 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25287 Z= 0.228 Angle : 0.659 10.871 34506 Z= 0.342 Chirality : 0.050 0.453 4032 Planarity : 0.005 0.040 4362 Dihedral : 6.582 58.753 4291 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.19 % Allowed : 11.45 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3015 helix: 1.80 (0.20), residues: 687 sheet: 0.83 (0.18), residues: 714 loop : -1.09 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 436 HIS 0.009 0.001 HIS A 207 PHE 0.036 0.002 PHE A 429 TYR 0.038 0.002 TYR C 904 ARG 0.005 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 42) link_NAG-ASN : angle 3.05900 ( 126) link_BETA1-4 : bond 0.00274 ( 6) link_BETA1-4 : angle 1.46873 ( 18) hydrogen bonds : bond 0.07275 ( 934) hydrogen bonds : angle 5.17331 ( 2559) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.61398 ( 78) covalent geometry : bond 0.00564 (25200) covalent geometry : angle 0.62905 (34284) ********************** 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 199 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8611 (m-80) cc_final: 0.8382 (m-80) REVERT: A 140 PHE cc_start: 0.7966 (p90) cc_final: 0.7558 (p90) REVERT: A 157 PHE cc_start: 0.9158 (m-80) cc_final: 0.8781 (p90) REVERT: A 160 TYR cc_start: 0.8105 (p90) cc_final: 0.7336 (p90) REVERT: A 374 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: A 409 GLN cc_start: 0.8754 (mt0) cc_final: 0.8147 (tt0) REVERT: A 421 TYR cc_start: 0.8643 (m-80) cc_final: 0.8345 (m-80) REVERT: A 955 ASN cc_start: 0.7861 (m-40) cc_final: 0.7527 (t0) REVERT: A 1038 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9087 (mmtp) REVERT: A 1123 SER cc_start: 0.8978 (m) cc_final: 0.8617 (p) REVERT: B 157 PHE cc_start: 0.9196 (m-80) cc_final: 0.8806 (p90) REVERT: B 160 TYR cc_start: 0.8234 (p90) cc_final: 0.7454 (p90) REVERT: B 200 TYR cc_start: 0.8179 (m-80) cc_final: 0.7935 (m-80) REVERT: B 421 TYR cc_start: 0.8727 (m-10) cc_final: 0.8356 (m-80) REVERT: B 453 TYR cc_start: 0.8400 (p90) cc_final: 0.7813 (p90) REVERT: B 955 ASN cc_start: 0.7815 (m-40) cc_final: 0.7433 (t0) REVERT: C 140 PHE cc_start: 0.7863 (p90) cc_final: 0.7296 (p90) REVERT: C 160 TYR cc_start: 0.8216 (p90) cc_final: 0.7610 (p90) REVERT: C 176 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7475 (mm) REVERT: C 421 TYR cc_start: 0.8744 (m-10) cc_final: 0.8152 (m-80) REVERT: C 423 TYR cc_start: 0.7962 (t80) cc_final: 0.7631 (t80) REVERT: C 955 ASN cc_start: 0.7714 (m-40) cc_final: 0.7275 (t0) outliers start: 32 outliers final: 22 residues processed: 185 average time/residue: 0.7857 time to fit residues: 185.6437 Evaluate side-chains 189 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 2.617 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE 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 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 C residue 101 ILE Chi-restraints excluded: chain C residue 117 LEU 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 565 PHE Chi-restraints excluded: chain C residue 569 ILE 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 104 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 131 optimal weight: 0.0030 chunk 276 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 207 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN 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 = 0.3922 r_free = 0.3922 target = 0.129377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072214 restraints weight = 43461.854| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.07 r_work: 0.2797 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25287 Z= 0.112 Angle : 0.569 10.737 34506 Z= 0.291 Chirality : 0.046 0.407 4032 Planarity : 0.004 0.037 4362 Dihedral : 6.333 59.952 4291 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.08 % Allowed : 11.63 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3015 helix: 2.03 (0.20), residues: 684 sheet: 1.17 (0.19), residues: 726 loop : -1.11 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 436 HIS 0.003 0.001 HIS B 207 PHE 0.028 0.001 PHE C 429 TYR 0.029 0.001 TYR C 453 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 42) link_NAG-ASN : angle 2.84329 ( 126) link_BETA1-4 : bond 0.00357 ( 6) link_BETA1-4 : angle 1.04378 ( 18) hydrogen bonds : bond 0.04937 ( 934) hydrogen bonds : angle 4.85878 ( 2559) SS BOND : bond 0.00326 ( 39) SS BOND : angle 1.05970 ( 78) covalent geometry : bond 0.00244 (25200) covalent geometry : angle 0.54172 (34284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23842.40 seconds wall clock time: 409 minutes 2.35 seconds (24542.35 seconds total)