Starting phenix.real_space_refine on Mon Aug 25 04:24:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jym_36726/08_2025/8jym_36726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jym_36726/08_2025/8jym_36726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jym_36726/08_2025/8jym_36726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jym_36726/08_2025/8jym_36726.map" model { file = "/net/cci-nas-00/data/ceres_data/8jym_36726/08_2025/8jym_36726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jym_36726/08_2025/8jym_36726.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 15897 2.51 5 N 4092 2.21 5 O 4827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24924 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8084 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: "D" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8084 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 7 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: "D" 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: "G" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8084 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 7 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: "G" 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: 4.75, per 1000 atoms: 0.19 Number of scatterers: 24924 At special positions: 0 Unit cell: (133.665, 140.7, 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 4827 8.00 N 4092 7.00 C 15897 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 D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.04 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " 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=3, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 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 B 1 " - " ASN A 717 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 616 " " NAG D1307 " - " ASN D 657 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D1074 " " NAG D1310 " - " ASN D1098 " " NAG D1311 " - " ASN D1134 " " NAG D1312 " - " ASN D 343 " " NAG E 1 " - " ASN D 717 " " NAG F 1 " - " ASN D 801 " " NAG G1301 " - " ASN G 61 " " NAG G1302 " - " ASN G 122 " " NAG G1303 " - " ASN G 165 " " NAG G1304 " - " ASN G 234 " " NAG G1305 " - " ASN G 282 " " NAG G1306 " - " ASN G 616 " " NAG G1307 " - " ASN G 657 " " NAG G1308 " - " ASN G 709 " " NAG G1309 " - " ASN G1074 " " NAG G1310 " - " ASN G1098 " " NAG G1311 " - " ASN G1134 " " NAG G1312 " - " ASN G 343 " " NAG H 1 " - " ASN G 717 " " NAG I 1 " - " ASN G 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 826.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5820 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 42 sheets defined 23.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.567A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.268A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.657A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) 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 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.745A 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 removed outlier: 3.514A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.157A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.711A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.950A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.106A 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 removed outlier: 3.508A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.214A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.567A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 337 through 342' Processing helix chain 'D' and resid 365 through 372 removed outlier: 4.268A pdb=" N ALA D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.657A pdb=" N SER D 408 " --> pdb=" O ASN D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 removed outlier: 3.514A pdb=" N GLY D 889 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 912 through 918 removed outlier: 4.158A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.711A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.949A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.214A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.566A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 365 through 372 removed outlier: 4.268A pdb=" N ALA G 372 " --> pdb=" O ILE G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.657A pdb=" N SER G 408 " --> pdb=" O ASN G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN G 762 " --> pdb=" O SER G 758 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 778 " --> pdb=" O GLN G 774 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 Processing helix chain 'G' and resid 866 through 884 Processing helix chain 'G' and resid 886 through 890 removed outlier: 3.514A pdb=" N GLY G 889 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 Processing helix chain 'G' and resid 912 through 918 removed outlier: 4.158A pdb=" N LEU G 916 " --> pdb=" O THR G 912 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 941 removed outlier: 3.711A pdb=" N ILE G 934 " --> pdb=" O ALA G 930 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR G 941 " --> pdb=" O SER G 937 " (cutoff:3.500A) Processing helix chain 'G' and resid 942 through 944 No H-bonds generated for 'chain 'G' and resid 942 through 944' Processing helix chain 'G' and resid 945 through 965 removed outlier: 3.950A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL G 952 " --> pdb=" O LEU G 948 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE G 980 " --> pdb=" O VAL G 976 " (cutoff:3.500A) Processing helix chain 'G' and resid 985 through 1033 removed outlier: 4.214A pdb=" N GLU G 990 " --> pdb=" O PRO G 986 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN G 992 " --> pdb=" O GLU G 988 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG G 995 " --> pdb=" O VAL G 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G1033 " --> pdb=" O MET G1029 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.955A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.767A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 624 through 626 removed outlier: 4.313A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.110A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.208A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=11, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.543A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=14, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=15, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.955A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 203 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.767A pdb=" N LEU D 241 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 624 through 626 removed outlier: 4.313A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=20, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.110A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=22, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=23, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.208A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'D' and resid 711 through 713 Processing sheet with id=25, first strand: chain 'D' and resid 717 through 728 removed outlier: 3.542A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 1120 through 1121 Processing sheet with id=28, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=29, first strand: chain 'G' and resid 25 through 30 removed outlier: 7.955A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 203 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'G' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.767A pdb=" N LEU G 241 " --> pdb=" O GLY G 103 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN G 121 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'G' and resid 624 through 626 removed outlier: 4.313A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 325 through 328 Processing sheet with id=34, first strand: chain 'G' and resid 354 through 358 removed outlier: 4.110A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=36, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=37, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.208A pdb=" N GLU G 654 " --> pdb=" O ALA G 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR G 696 " --> pdb=" O GLU G 654 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'G' and resid 711 through 713 Processing sheet with id=39, first strand: chain 'G' and resid 717 through 728 removed outlier: 3.542A pdb=" N MET G1050 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 1120 through 1121 Processing sheet with id=42, first strand: chain 'G' and resid 1094 through 1097 939 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 2.25 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: 7892 1.34 - 1.46: 6261 1.46 - 1.58: 11206 1.58 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 25494 Sorted by residual: bond pdb=" C1 NAG D1309 " pdb=" O5 NAG D1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG G1309 " pdb=" O5 NAG G1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C1 NAG G1301 " pdb=" O5 NAG G1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 25489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 32931 1.11 - 2.22: 1340 2.22 - 3.33: 362 3.33 - 4.44: 41 4.44 - 5.55: 21 Bond angle restraints: 34695 Sorted by residual: angle pdb=" N GLN D1002 " pdb=" CA GLN D1002 " pdb=" CB GLN D1002 " ideal model delta sigma weight residual 110.28 115.46 -5.18 1.55e+00 4.16e-01 1.12e+01 angle pdb=" N GLN G1002 " pdb=" CA GLN G1002 " pdb=" CB GLN G1002 " ideal model delta sigma weight residual 110.28 115.46 -5.18 1.55e+00 4.16e-01 1.12e+01 angle pdb=" N GLN A1002 " pdb=" CA GLN A1002 " pdb=" CB GLN A1002 " ideal model delta sigma weight residual 110.28 115.45 -5.17 1.55e+00 4.16e-01 1.11e+01 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 117.89 -5.55 2.04e+00 2.40e-01 7.39e+00 angle pdb=" N GLY D 526 " pdb=" CA GLY D 526 " pdb=" C GLY D 526 " ideal model delta sigma weight residual 112.34 117.88 -5.54 2.04e+00 2.40e-01 7.37e+00 ... (remaining 34690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 14441 17.70 - 35.40: 1159 35.40 - 53.09: 171 53.09 - 70.79: 36 70.79 - 88.49: 24 Dihedral angle restraints: 15831 sinusoidal: 6795 harmonic: 9036 Sorted by residual: dihedral pdb=" CB CYS D 480 " pdb=" SG CYS D 480 " pdb=" SG CYS D 488 " pdb=" CB CYS D 488 " ideal model delta sinusoidal sigma weight residual 93.00 37.75 55.25 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 37.76 55.24 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual 93.00 37.77 55.23 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 15828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2830 0.040 - 0.079: 809 0.079 - 0.119: 389 0.119 - 0.158: 49 0.158 - 0.198: 3 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C1 NAG D1308 " pdb=" ND2 ASN D 709 " pdb=" C2 NAG D1308 " pdb=" O5 NAG D1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" C1 NAG G1308 " pdb=" ND2 ASN G 709 " pdb=" C2 NAG G1308 " pdb=" O5 NAG G1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 4077 not shown) Planarity restraints: 4458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 906 " -0.013 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE D 906 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE D 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 906 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.013 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE A 906 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 906 " 0.013 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE G 906 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE G 906 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 906 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 906 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 906 " 0.000 2.00e-02 2.50e+03 ... (remaining 4455 not shown) Histogram of nonbonded interaction distances: 0.71 - 1.55: 36 1.55 - 2.38: 114 2.38 - 3.22: 22720 3.22 - 4.06: 57345 4.06 - 4.90: 108318 Warning: very small nonbonded interaction distances. Nonbonded interactions: 188533 Sorted by model distance: nonbonded pdb=" NH1 ARG A 983 " pdb=" CA VAL D 382 " model vdw 0.706 3.550 nonbonded pdb=" CA VAL A 382 " pdb=" NH1 ARG G 983 " model vdw 0.706 3.550 nonbonded pdb=" NH1 ARG D 983 " pdb=" CA VAL G 382 " model vdw 0.707 3.550 nonbonded pdb=" O LYS A 41 " pdb=" OE1 GLN D 563 " model vdw 0.852 3.040 nonbonded pdb=" OE1 GLN A 563 " pdb=" O LYS G 41 " model vdw 0.852 3.040 ... (remaining 188528 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.890 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.004 0.060 25584 Z= 0.186 Angle : 0.565 5.547 34917 Z= 0.290 Chirality : 0.045 0.198 4080 Planarity : 0.004 0.037 4416 Dihedral : 12.783 88.491 9894 Min Nonbonded Distance : 0.706 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3051 helix: 2.27 (0.22), residues: 612 sheet: 0.97 (0.20), residues: 666 loop : -1.05 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1039 TYR 0.015 0.001 TYR D1067 PHE 0.031 0.001 PHE D 906 TRP 0.004 0.001 TRP A 886 HIS 0.002 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00383 (25494) covalent geometry : angle 0.55127 (34695) SS BOND : bond 0.00407 ( 39) SS BOND : angle 1.49281 ( 78) hydrogen bonds : bond 0.11035 ( 939) hydrogen bonds : angle 5.56400 ( 2574) Misc. bond : bond 0.05996 ( 3) link_BETA1-4 : bond 0.00381 ( 6) link_BETA1-4 : angle 0.96823 ( 18) link_NAG-ASN : bond 0.00230 ( 42) link_NAG-ASN : angle 1.76644 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.667 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 351 TYR cc_start: 0.8151 (p90) cc_final: 0.7420 (p90) REVERT: A 586 ASP cc_start: 0.7772 (m-30) cc_final: 0.7553 (m-30) REVERT: A 979 ASP cc_start: 0.8141 (t70) cc_final: 0.7889 (t0) REVERT: A 985 ASP cc_start: 0.8106 (p0) cc_final: 0.7825 (p0) REVERT: D 351 TYR cc_start: 0.8276 (p90) cc_final: 0.7526 (p90) REVERT: D 586 ASP cc_start: 0.7663 (m-30) cc_final: 0.7339 (m-30) REVERT: D 755 GLN cc_start: 0.9178 (mt0) cc_final: 0.8956 (mt0) REVERT: D 979 ASP cc_start: 0.7981 (t70) cc_final: 0.7733 (t0) REVERT: D 985 ASP cc_start: 0.8128 (p0) cc_final: 0.7834 (p0) REVERT: G 351 TYR cc_start: 0.8255 (p90) cc_final: 0.7564 (p90) REVERT: G 979 ASP cc_start: 0.8192 (t70) cc_final: 0.7970 (t0) REVERT: G 985 ASP cc_start: 0.8102 (p0) cc_final: 0.7872 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.5590 time to fit residues: 122.9102 Evaluate side-chains 120 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 856 ASN A1010 GLN D 339 HIS ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN D1010 GLN G 339 HIS ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN G 856 ASN G1010 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.123404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072143 restraints weight = 48876.962| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.03 r_work: 0.2857 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25584 Z= 0.133 Angle : 0.549 6.543 34917 Z= 0.289 Chirality : 0.045 0.208 4080 Planarity : 0.004 0.050 4416 Dihedral : 7.122 55.964 4329 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.55 % Allowed : 6.45 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3051 helix: 2.47 (0.22), residues: 612 sheet: 0.99 (0.20), residues: 693 loop : -1.12 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 983 TYR 0.018 0.001 TYR G 160 PHE 0.019 0.001 PHE A 906 TRP 0.022 0.002 TRP A 436 HIS 0.003 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00308 (25494) covalent geometry : angle 0.53662 (34695) SS BOND : bond 0.00214 ( 39) SS BOND : angle 1.21485 ( 78) hydrogen bonds : bond 0.05353 ( 939) hydrogen bonds : angle 4.97089 ( 2574) Misc. bond : bond 0.00242 ( 3) link_BETA1-4 : bond 0.00394 ( 6) link_BETA1-4 : angle 0.84209 ( 18) link_NAG-ASN : bond 0.00249 ( 42) link_NAG-ASN : angle 1.81162 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7913 (p90) cc_final: 0.7492 (p90) REVERT: A 586 ASP cc_start: 0.7815 (m-30) cc_final: 0.7614 (m-30) REVERT: A 624 ILE cc_start: 0.8457 (pt) cc_final: 0.8052 (pp) REVERT: A 979 ASP cc_start: 0.8067 (t70) cc_final: 0.7802 (t0) REVERT: D 335 LEU cc_start: 0.8412 (mm) cc_final: 0.8022 (tm) REVERT: D 351 TYR cc_start: 0.8035 (p90) cc_final: 0.7602 (p90) REVERT: D 586 ASP cc_start: 0.7754 (m-30) cc_final: 0.7452 (m-30) REVERT: D 979 ASP cc_start: 0.8078 (t70) cc_final: 0.7809 (t0) REVERT: G 351 TYR cc_start: 0.8065 (p90) cc_final: 0.7645 (p90) REVERT: G 429 PHE cc_start: 0.8285 (t80) cc_final: 0.7989 (t80) REVERT: G 624 ILE cc_start: 0.8431 (pt) cc_final: 0.8135 (pp) REVERT: G 979 ASP cc_start: 0.8171 (t70) cc_final: 0.7907 (t0) outliers start: 15 outliers final: 4 residues processed: 145 average time/residue: 0.4722 time to fit residues: 81.3786 Evaluate side-chains 127 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain D residue 258 TRP Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 1002 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 298 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 613 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.123546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072206 restraints weight = 48692.861| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.02 r_work: 0.2858 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25584 Z= 0.121 Angle : 0.517 6.391 34917 Z= 0.271 Chirality : 0.044 0.211 4080 Planarity : 0.004 0.038 4416 Dihedral : 6.812 56.102 4329 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.85 % Allowed : 7.82 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.15), residues: 3051 helix: 2.56 (0.22), residues: 612 sheet: 1.09 (0.20), residues: 681 loop : -1.12 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.017 0.001 TYR D1067 PHE 0.017 0.001 PHE A 906 TRP 0.019 0.001 TRP D 436 HIS 0.003 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00283 (25494) covalent geometry : angle 0.50454 (34695) SS BOND : bond 0.00193 ( 39) SS BOND : angle 1.10738 ( 78) hydrogen bonds : bond 0.05064 ( 939) hydrogen bonds : angle 4.81973 ( 2574) Misc. bond : bond 0.00302 ( 3) link_BETA1-4 : bond 0.00295 ( 6) link_BETA1-4 : angle 0.82817 ( 18) link_NAG-ASN : bond 0.00251 ( 42) link_NAG-ASN : angle 1.78009 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8429 (pt) cc_final: 0.8032 (pp) REVERT: A 979 ASP cc_start: 0.8153 (t70) cc_final: 0.7805 (t0) REVERT: A 988 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 335 LEU cc_start: 0.8395 (mm) cc_final: 0.7992 (tm) REVERT: D 586 ASP cc_start: 0.7779 (m-30) cc_final: 0.7497 (m-30) REVERT: D 979 ASP cc_start: 0.8199 (t70) cc_final: 0.7743 (t0) REVERT: G 342 PHE cc_start: 0.8525 (m-80) cc_final: 0.8225 (m-80) REVERT: G 351 TYR cc_start: 0.8060 (p90) cc_final: 0.7627 (p90) REVERT: G 429 PHE cc_start: 0.8254 (t80) cc_final: 0.7967 (t80) REVERT: G 624 ILE cc_start: 0.8496 (pt) cc_final: 0.8196 (pp) REVERT: G 979 ASP cc_start: 0.8247 (t70) cc_final: 0.7878 (t0) outliers start: 23 outliers final: 7 residues processed: 142 average time/residue: 0.5666 time to fit residues: 93.5956 Evaluate side-chains 126 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 258 TRP Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 780 GLU Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 294 optimal weight: 0.7980 chunk 217 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 152 optimal weight: 4.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072421 restraints weight = 48469.386| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.00 r_work: 0.2859 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25584 Z= 0.116 Angle : 0.512 7.409 34917 Z= 0.266 Chirality : 0.044 0.212 4080 Planarity : 0.005 0.199 4416 Dihedral : 6.674 56.321 4329 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.77 % Allowed : 9.33 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3051 helix: 2.63 (0.22), residues: 612 sheet: 1.09 (0.20), residues: 681 loop : -1.10 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 983 TYR 0.017 0.001 TYR D1067 PHE 0.019 0.001 PHE A 133 TRP 0.013 0.001 TRP D 436 HIS 0.003 0.000 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00267 (25494) covalent geometry : angle 0.49977 (34695) SS BOND : bond 0.00186 ( 39) SS BOND : angle 1.02209 ( 78) hydrogen bonds : bond 0.04903 ( 939) hydrogen bonds : angle 4.71744 ( 2574) Misc. bond : bond 0.00949 ( 3) link_BETA1-4 : bond 0.00311 ( 6) link_BETA1-4 : angle 0.80729 ( 18) link_NAG-ASN : bond 0.00251 ( 42) link_NAG-ASN : angle 1.76858 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8401 (pt) cc_final: 0.8015 (pp) REVERT: A 979 ASP cc_start: 0.8236 (t70) cc_final: 0.7799 (OUTLIER) REVERT: A 988 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 335 LEU cc_start: 0.8392 (mm) cc_final: 0.7996 (tm) REVERT: D 586 ASP cc_start: 0.7759 (m-30) cc_final: 0.7483 (m-30) REVERT: D 979 ASP cc_start: 0.8265 (t70) cc_final: 0.7654 (t0) REVERT: G 342 PHE cc_start: 0.8528 (m-80) cc_final: 0.8226 (m-80) REVERT: G 351 TYR cc_start: 0.8067 (p90) cc_final: 0.7635 (p90) REVERT: G 429 PHE cc_start: 0.8272 (t80) cc_final: 0.8006 (t80) REVERT: G 624 ILE cc_start: 0.8445 (pt) cc_final: 0.8136 (pp) REVERT: G 979 ASP cc_start: 0.8307 (t70) cc_final: 0.7905 (t0) outliers start: 21 outliers final: 11 residues processed: 138 average time/residue: 0.5292 time to fit residues: 85.9453 Evaluate side-chains 128 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain G residue 258 TRP Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 780 GLU Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 195 optimal weight: 0.5980 chunk 239 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 286 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 72 optimal weight: 0.0010 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.124366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073029 restraints weight = 48577.571| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.01 r_work: 0.2873 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25584 Z= 0.103 Angle : 0.509 7.370 34917 Z= 0.263 Chirality : 0.044 0.267 4080 Planarity : 0.004 0.086 4416 Dihedral : 7.042 171.569 4329 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.00 % Allowed : 10.29 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3051 helix: 2.71 (0.22), residues: 612 sheet: 1.13 (0.20), residues: 666 loop : -1.06 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.000 ARG D 983 TYR 0.016 0.001 TYR D1067 PHE 0.027 0.001 PHE D 342 TRP 0.012 0.001 TRP D 436 HIS 0.002 0.000 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00224 (25494) covalent geometry : angle 0.49710 (34695) SS BOND : bond 0.00182 ( 39) SS BOND : angle 0.93130 ( 78) hydrogen bonds : bond 0.04560 ( 939) hydrogen bonds : angle 4.63481 ( 2574) Misc. bond : bond 0.00752 ( 3) link_BETA1-4 : bond 0.00333 ( 6) link_BETA1-4 : angle 0.79413 ( 18) link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 1.74932 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8367 (pt) cc_final: 0.7986 (pp) REVERT: A 979 ASP cc_start: 0.8285 (t70) cc_final: 0.7879 (OUTLIER) REVERT: A 988 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8564 (tm-30) REVERT: D 586 ASP cc_start: 0.7775 (m-30) cc_final: 0.7513 (m-30) REVERT: D 979 ASP cc_start: 0.8293 (t70) cc_final: 0.7916 (t0) REVERT: G 342 PHE cc_start: 0.8519 (m-80) cc_final: 0.8221 (m-80) REVERT: G 351 TYR cc_start: 0.8077 (p90) cc_final: 0.7611 (p90) REVERT: G 429 PHE cc_start: 0.8239 (t80) cc_final: 0.7998 (t80) REVERT: G 624 ILE cc_start: 0.8436 (pt) cc_final: 0.8111 (pp) REVERT: G 979 ASP cc_start: 0.8320 (t70) cc_final: 0.7991 (t0) outliers start: 27 outliers final: 10 residues processed: 151 average time/residue: 0.5325 time to fit residues: 95.0985 Evaluate side-chains 130 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN D 409 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071916 restraints weight = 48596.003| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.01 r_work: 0.2854 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25584 Z= 0.139 Angle : 0.574 20.680 34917 Z= 0.293 Chirality : 0.045 0.202 4080 Planarity : 0.005 0.162 4416 Dihedral : 7.299 163.098 4329 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.74 % Allowed : 11.14 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 3051 helix: 2.68 (0.22), residues: 612 sheet: 1.04 (0.20), residues: 669 loop : -1.07 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 983 TYR 0.017 0.001 TYR D1067 PHE 0.026 0.001 PHE D 342 TRP 0.010 0.001 TRP D 436 HIS 0.003 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00328 (25494) covalent geometry : angle 0.56341 (34695) SS BOND : bond 0.00185 ( 39) SS BOND : angle 1.10922 ( 78) hydrogen bonds : bond 0.05071 ( 939) hydrogen bonds : angle 4.69639 ( 2574) Misc. bond : bond 0.00891 ( 3) link_BETA1-4 : bond 0.00255 ( 6) link_BETA1-4 : angle 0.81453 ( 18) link_NAG-ASN : bond 0.00255 ( 42) link_NAG-ASN : angle 1.73657 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7899 (p90) cc_final: 0.7474 (p90) REVERT: A 624 ILE cc_start: 0.8349 (pt) cc_final: 0.7967 (pp) REVERT: A 979 ASP cc_start: 0.8481 (t70) cc_final: 0.8188 (t0) REVERT: A 988 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8554 (tm-30) REVERT: D 586 ASP cc_start: 0.7733 (m-30) cc_final: 0.7458 (m-30) REVERT: D 979 ASP cc_start: 0.8290 (t70) cc_final: 0.8009 (t0) REVERT: G 342 PHE cc_start: 0.8532 (m-80) cc_final: 0.8255 (m-80) REVERT: G 351 TYR cc_start: 0.8072 (p90) cc_final: 0.7640 (p90) REVERT: G 429 PHE cc_start: 0.8279 (t80) cc_final: 0.7989 (t80) REVERT: G 624 ILE cc_start: 0.8414 (pt) cc_final: 0.8107 (pp) REVERT: G 979 ASP cc_start: 0.8495 (t70) cc_final: 0.8290 (t0) outliers start: 20 outliers final: 10 residues processed: 138 average time/residue: 0.5496 time to fit residues: 89.3073 Evaluate side-chains 131 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 242 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 294 optimal weight: 0.0000 chunk 97 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 239 optimal weight: 8.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071858 restraints weight = 48500.806| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.00 r_work: 0.2847 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25584 Z= 0.142 Angle : 0.603 27.656 34917 Z= 0.304 Chirality : 0.045 0.304 4080 Planarity : 0.010 0.427 4416 Dihedral : 7.268 177.324 4329 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.77 % Allowed : 11.54 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3051 helix: 2.64 (0.22), residues: 612 sheet: 1.03 (0.20), residues: 669 loop : -1.06 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG G 983 TYR 0.017 0.001 TYR D1067 PHE 0.026 0.001 PHE D 342 TRP 0.009 0.001 TRP D 436 HIS 0.003 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00335 (25494) covalent geometry : angle 0.59338 (34695) SS BOND : bond 0.00168 ( 39) SS BOND : angle 1.11994 ( 78) hydrogen bonds : bond 0.05196 ( 939) hydrogen bonds : angle 4.70382 ( 2574) Misc. bond : bond 0.01336 ( 3) link_BETA1-4 : bond 0.00247 ( 6) link_BETA1-4 : angle 0.84938 ( 18) link_NAG-ASN : bond 0.00250 ( 42) link_NAG-ASN : angle 1.75302 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7901 (p90) cc_final: 0.7480 (p90) REVERT: A 624 ILE cc_start: 0.8360 (pt) cc_final: 0.7980 (pp) REVERT: A 979 ASP cc_start: 0.8514 (t70) cc_final: 0.8116 (t0) REVERT: A 988 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8599 (tm-30) REVERT: D 335 LEU cc_start: 0.8387 (mm) cc_final: 0.8018 (tm) REVERT: D 586 ASP cc_start: 0.7734 (m-30) cc_final: 0.7451 (m-30) REVERT: D 979 ASP cc_start: 0.8377 (t70) cc_final: 0.7975 (t0) REVERT: G 342 PHE cc_start: 0.8531 (m-80) cc_final: 0.8268 (m-80) REVERT: G 351 TYR cc_start: 0.8071 (p90) cc_final: 0.7632 (p90) REVERT: G 429 PHE cc_start: 0.8266 (t80) cc_final: 0.7992 (t80) REVERT: G 624 ILE cc_start: 0.8392 (pt) cc_final: 0.8060 (pp) REVERT: G 979 ASP cc_start: 0.8620 (t70) cc_final: 0.8223 (t0) outliers start: 21 outliers final: 10 residues processed: 143 average time/residue: 0.5205 time to fit residues: 88.3684 Evaluate side-chains 127 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 77 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 265 optimal weight: 0.0170 chunk 113 optimal weight: 5.9990 chunk 81 optimal weight: 0.0470 chunk 82 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073351 restraints weight = 48319.977| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.97 r_work: 0.2879 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 25584 Z= 0.105 Angle : 0.526 9.927 34917 Z= 0.270 Chirality : 0.044 0.218 4080 Planarity : 0.005 0.142 4416 Dihedral : 6.959 164.161 4329 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.66 % Allowed : 11.91 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3051 helix: 2.67 (0.22), residues: 615 sheet: 1.08 (0.20), residues: 669 loop : -1.00 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG G 983 TYR 0.016 0.001 TYR D1067 PHE 0.026 0.001 PHE D 342 TRP 0.011 0.001 TRP D 436 HIS 0.002 0.000 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00228 (25494) covalent geometry : angle 0.51498 (34695) SS BOND : bond 0.00181 ( 39) SS BOND : angle 0.93985 ( 78) hydrogen bonds : bond 0.04494 ( 939) hydrogen bonds : angle 4.69097 ( 2574) Misc. bond : bond 0.00778 ( 3) link_BETA1-4 : bond 0.00337 ( 6) link_BETA1-4 : angle 0.74925 ( 18) link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 1.73597 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8381 (pt) cc_final: 0.7963 (pp) REVERT: A 979 ASP cc_start: 0.8429 (t70) cc_final: 0.8052 (t0) REVERT: A 988 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8628 (tm-30) REVERT: D 335 LEU cc_start: 0.8405 (mm) cc_final: 0.8037 (tm) REVERT: D 586 ASP cc_start: 0.7744 (m-30) cc_final: 0.7483 (m-30) REVERT: D 979 ASP cc_start: 0.8379 (t70) cc_final: 0.7962 (t0) REVERT: G 342 PHE cc_start: 0.8523 (m-80) cc_final: 0.8263 (m-80) REVERT: G 351 TYR cc_start: 0.8077 (p90) cc_final: 0.7619 (p90) REVERT: G 367 VAL cc_start: 0.8332 (m) cc_final: 0.8082 (p) REVERT: G 429 PHE cc_start: 0.8207 (t80) cc_final: 0.7951 (t80) REVERT: G 624 ILE cc_start: 0.8394 (pt) cc_final: 0.8061 (pp) REVERT: G 979 ASP cc_start: 0.8506 (t70) cc_final: 0.8240 (t0) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 0.5514 time to fit residues: 90.8533 Evaluate side-chains 125 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain G residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 59 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 175 optimal weight: 0.1980 chunk 190 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.124448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072995 restraints weight = 48580.152| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.01 r_work: 0.2878 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25584 Z= 0.107 Angle : 0.538 10.525 34917 Z= 0.276 Chirality : 0.044 0.211 4080 Planarity : 0.005 0.117 4416 Dihedral : 5.861 56.562 4329 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.63 % Allowed : 12.24 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3051 helix: 2.75 (0.22), residues: 612 sheet: 1.06 (0.20), residues: 669 loop : -1.01 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG A 983 TYR 0.016 0.001 TYR D1067 PHE 0.026 0.001 PHE D 342 TRP 0.010 0.001 TRP D 436 HIS 0.002 0.000 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00244 (25494) covalent geometry : angle 0.52715 (34695) SS BOND : bond 0.00194 ( 39) SS BOND : angle 0.97835 ( 78) hydrogen bonds : bond 0.04558 ( 939) hydrogen bonds : angle 4.64623 ( 2574) Misc. bond : bond 0.00427 ( 3) link_BETA1-4 : bond 0.00298 ( 6) link_BETA1-4 : angle 0.80045 ( 18) link_NAG-ASN : bond 0.00255 ( 42) link_NAG-ASN : angle 1.69495 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8317 (t70) cc_final: 0.8020 (t0) REVERT: A 988 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8633 (tm-30) REVERT: D 586 ASP cc_start: 0.7714 (m-30) cc_final: 0.7480 (m-30) REVERT: D 979 ASP cc_start: 0.8393 (t70) cc_final: 0.8008 (t0) REVERT: G 351 TYR cc_start: 0.8078 (p90) cc_final: 0.7622 (p90) REVERT: G 367 VAL cc_start: 0.8324 (m) cc_final: 0.8079 (p) REVERT: G 429 PHE cc_start: 0.8183 (t80) cc_final: 0.7967 (t80) REVERT: G 624 ILE cc_start: 0.8428 (pt) cc_final: 0.8095 (pp) outliers start: 17 outliers final: 10 residues processed: 127 average time/residue: 0.5960 time to fit residues: 88.2764 Evaluate side-chains 119 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 31 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 157 optimal weight: 0.0870 chunk 192 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.122916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070996 restraints weight = 48673.110| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.01 r_work: 0.2826 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25584 Z= 0.181 Angle : 0.620 27.262 34917 Z= 0.318 Chirality : 0.046 0.211 4080 Planarity : 0.006 0.211 4416 Dihedral : 6.437 156.480 4329 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.52 % Allowed : 12.35 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.15), residues: 3051 helix: 2.62 (0.21), residues: 615 sheet: 0.94 (0.20), residues: 669 loop : -1.09 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 983 TYR 0.018 0.001 TYR D1067 PHE 0.026 0.001 PHE D 342 TRP 0.006 0.001 TRP A 258 HIS 0.005 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00443 (25494) covalent geometry : angle 0.60985 (34695) SS BOND : bond 0.00227 ( 39) SS BOND : angle 1.27120 ( 78) hydrogen bonds : bond 0.05602 ( 939) hydrogen bonds : angle 4.78756 ( 2574) Misc. bond : bond 0.01009 ( 3) link_BETA1-4 : bond 0.00151 ( 6) link_BETA1-4 : angle 0.88277 ( 18) link_NAG-ASN : bond 0.00274 ( 42) link_NAG-ASN : angle 1.74053 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7922 (p90) cc_final: 0.7474 (p90) REVERT: A 367 VAL cc_start: 0.8325 (m) cc_final: 0.8100 (p) REVERT: A 979 ASP cc_start: 0.8599 (t70) cc_final: 0.8279 (t0) REVERT: A 988 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8613 (tm-30) REVERT: D 335 LEU cc_start: 0.8427 (mm) cc_final: 0.8057 (tm) REVERT: D 367 VAL cc_start: 0.8402 (m) cc_final: 0.8166 (p) REVERT: D 586 ASP cc_start: 0.7781 (m-30) cc_final: 0.7432 (m-30) REVERT: D 979 ASP cc_start: 0.8389 (t70) cc_final: 0.8080 (t0) REVERT: G 351 TYR cc_start: 0.8068 (p90) cc_final: 0.7606 (p90) REVERT: G 367 VAL cc_start: 0.8290 (m) cc_final: 0.8049 (p) REVERT: G 429 PHE cc_start: 0.8179 (t80) cc_final: 0.7883 (t80) REVERT: G 624 ILE cc_start: 0.8377 (pt) cc_final: 0.8084 (pp) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.5050 time to fit residues: 75.0096 Evaluate side-chains 119 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 274 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 174 optimal weight: 0.0770 chunk 264 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.123999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072151 restraints weight = 48538.540| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.02 r_work: 0.2865 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25584 Z= 0.114 Angle : 0.637 35.751 34917 Z= 0.319 Chirality : 0.044 0.284 4080 Planarity : 0.008 0.422 4416 Dihedral : 6.132 120.645 4329 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.63 % Allowed : 12.39 % Favored : 86.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3051 helix: 2.64 (0.22), residues: 615 sheet: 0.99 (0.20), residues: 669 loop : -1.02 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG D 983 TYR 0.015 0.001 TYR D1067 PHE 0.025 0.001 PHE D 342 TRP 0.010 0.001 TRP D 436 HIS 0.002 0.000 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00255 (25494) covalent geometry : angle 0.62834 (34695) SS BOND : bond 0.00183 ( 39) SS BOND : angle 1.00530 ( 78) hydrogen bonds : bond 0.04782 ( 939) hydrogen bonds : angle 4.71866 ( 2574) Misc. bond : bond 0.01134 ( 3) link_BETA1-4 : bond 0.00398 ( 6) link_BETA1-4 : angle 0.76671 ( 18) link_NAG-ASN : bond 0.00250 ( 42) link_NAG-ASN : angle 1.75480 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9178.70 seconds wall clock time: 156 minutes 26.89 seconds (9386.89 seconds total)