Starting phenix.real_space_refine on Sat Jun 21 21:23:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jym_36726/06_2025/8jym_36726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jym_36726/06_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_36726/06_2025/8jym_36726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jym_36726/06_2025/8jym_36726.map" model { file = "/net/cci-nas-00/data/ceres_data/8jym_36726/06_2025/8jym_36726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jym_36726/06_2025/8jym_36726.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.68, per 1000 atoms: 0.63 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: 6.23 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 3.23 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: 12.03 Time building geometry restraints manager: 7.46 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: 0.00 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: 9.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.090 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 61.080 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.290 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (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 TRP 0.004 0.001 TRP A 886 HIS 0.002 0.001 HIS G1064 PHE 0.031 0.001 PHE D 906 TYR 0.015 0.001 TYR D1067 ARG 0.001 0.000 ARG D1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 42) link_NAG-ASN : angle 1.76644 ( 126) link_BETA1-4 : bond 0.00381 ( 6) link_BETA1-4 : angle 0.96823 ( 18) hydrogen bonds : bond 0.11035 ( 939) hydrogen bonds : angle 5.56400 ( 2574) SS BOND : bond 0.00407 ( 39) SS BOND : angle 1.49281 ( 78) covalent geometry : bond 0.00383 (25494) covalent geometry : angle 0.55127 (34695) Misc. bond : bond 0.05996 ( 3) *********************** 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 : 2.657 Fit side-chains 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: 0.7839 (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: 0.7848 (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: 0.7886 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 1.2544 time to fit residues: 279.1663 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 : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 242 optimal weight: 0.0470 chunk 93 optimal weight: 0.0020 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 overall best weight: 0.4488 ------------------------------------------------------------------------------- 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 613 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.124431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.073491 restraints weight = 48618.018| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.02 r_work: 0.2885 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25584 Z= 0.112 Angle : 0.535 6.476 34917 Z= 0.281 Chirality : 0.044 0.224 4080 Planarity : 0.004 0.051 4416 Dihedral : 7.048 55.602 4329 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.63 % Allowed : 5.68 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3051 helix: 2.54 (0.22), residues: 612 sheet: 1.08 (0.20), residues: 687 loop : -1.06 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 436 HIS 0.002 0.000 HIS D1088 PHE 0.016 0.001 PHE D 429 TYR 0.018 0.001 TYR A 160 ARG 0.014 0.000 ARG G 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 42) link_NAG-ASN : angle 1.78018 ( 126) link_BETA1-4 : bond 0.00476 ( 6) link_BETA1-4 : angle 0.76437 ( 18) hydrogen bonds : bond 0.04847 ( 939) hydrogen bonds : angle 4.90940 ( 2574) SS BOND : bond 0.00205 ( 39) SS BOND : angle 1.07503 ( 78) covalent geometry : bond 0.00241 (25494) covalent geometry : angle 0.52293 (34695) Misc. bond : bond 0.00441 ( 3) *********************** 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 162 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7912 (p90) cc_final: 0.7486 (p90) REVERT: A 979 ASP cc_start: 0.8065 (t70) cc_final: 0.7797 (t0) REVERT: D 53 ASP cc_start: 0.8202 (t0) cc_final: 0.7969 (t0) REVERT: D 335 LEU cc_start: 0.8412 (mm) cc_final: 0.8020 (tm) REVERT: D 351 TYR cc_start: 0.8046 (p90) cc_final: 0.7610 (p90) REVERT: D 586 ASP cc_start: 0.7714 (m-30) cc_final: 0.7442 (m-30) REVERT: D 855 PHE cc_start: 0.7715 (m-80) cc_final: 0.7306 (m-80) REVERT: D 979 ASP cc_start: 0.8056 (t70) cc_final: 0.7785 (t0) REVERT: G 351 TYR cc_start: 0.8081 (p90) cc_final: 0.7654 (p90) REVERT: G 429 PHE cc_start: 0.8274 (t80) cc_final: 0.7910 (t80) REVERT: G 624 ILE cc_start: 0.8436 (pt) cc_final: 0.8084 (pp) REVERT: G 780 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8616 (pt0) REVERT: G 979 ASP cc_start: 0.8160 (t70) cc_final: 0.7895 (t0) outliers start: 17 outliers final: 5 residues processed: 149 average time/residue: 1.2103 time to fit residues: 216.9469 Evaluate side-chains 134 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 4.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 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 1002 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 227 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.0770 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.071346 restraints weight = 48691.019| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.02 r_work: 0.2835 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25584 Z= 0.148 Angle : 0.531 5.982 34917 Z= 0.279 Chirality : 0.045 0.197 4080 Planarity : 0.004 0.036 4416 Dihedral : 6.814 56.703 4329 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.92 % Allowed : 7.82 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3051 helix: 2.54 (0.22), residues: 612 sheet: 1.05 (0.20), residues: 681 loop : -1.13 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 436 HIS 0.005 0.001 HIS G1064 PHE 0.024 0.001 PHE A 906 TYR 0.018 0.001 TYR D1067 ARG 0.007 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 1.77847 ( 126) link_BETA1-4 : bond 0.00238 ( 6) link_BETA1-4 : angle 0.87724 ( 18) hydrogen bonds : bond 0.05478 ( 939) hydrogen bonds : angle 4.84947 ( 2574) SS BOND : bond 0.00216 ( 39) SS BOND : angle 1.22869 ( 78) covalent geometry : bond 0.00357 (25494) covalent geometry : angle 0.51865 (34695) Misc. bond : bond 0.00194 ( 3) *********************** 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: 25 poor density : 128 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8474 (pt) cc_final: 0.8070 (pp) REVERT: A 979 ASP cc_start: 0.8229 (t70) cc_final: 0.7863 (t0) REVERT: A 988 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8592 (tm-30) REVERT: D 53 ASP cc_start: 0.8191 (t0) cc_final: 0.7943 (t0) REVERT: D 335 LEU cc_start: 0.8395 (mm) cc_final: 0.7994 (tm) REVERT: D 586 ASP cc_start: 0.7800 (m-30) cc_final: 0.7516 (m-30) REVERT: D 979 ASP cc_start: 0.8248 (t70) cc_final: 0.7863 (t0) REVERT: G 342 PHE cc_start: 0.8527 (m-80) cc_final: 0.8219 (m-80) REVERT: G 351 TYR cc_start: 0.8066 (p90) cc_final: 0.7636 (p90) REVERT: G 429 PHE cc_start: 0.8264 (t80) cc_final: 0.7989 (t80) REVERT: G 624 ILE cc_start: 0.8470 (pt) cc_final: 0.8165 (pp) REVERT: G 979 ASP cc_start: 0.8305 (t70) cc_final: 0.7960 (t0) outliers start: 25 outliers final: 7 residues processed: 143 average time/residue: 1.8852 time to fit residues: 322.7025 Evaluate side-chains 125 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 4.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 524 VAL 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 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 21 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.123342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.071874 restraints weight = 48718.028| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.02 r_work: 0.2847 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1129 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= 0.126 Angle : 0.518 7.609 34917 Z= 0.270 Chirality : 0.044 0.208 4080 Planarity : 0.004 0.044 4416 Dihedral : 6.676 56.463 4329 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.74 % Allowed : 9.55 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3051 helix: 2.61 (0.22), residues: 612 sheet: 1.05 (0.20), residues: 681 loop : -1.11 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.003 0.001 HIS G1064 PHE 0.015 0.001 PHE A 906 TYR 0.017 0.001 TYR D1067 ARG 0.005 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 42) link_NAG-ASN : angle 1.77904 ( 126) link_BETA1-4 : bond 0.00331 ( 6) link_BETA1-4 : angle 0.81548 ( 18) hydrogen bonds : bond 0.05139 ( 939) hydrogen bonds : angle 4.73501 ( 2574) SS BOND : bond 0.00187 ( 39) SS BOND : angle 1.08253 ( 78) covalent geometry : bond 0.00294 (25494) covalent geometry : angle 0.50521 (34695) Misc. bond : bond 0.00765 ( 3) *********************** 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 146 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8383 (pt) cc_final: 0.7993 (pp) REVERT: A 979 ASP cc_start: 0.8258 (t70) cc_final: 0.7945 (OUTLIER) REVERT: A 988 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8587 (tm-30) REVERT: D 53 ASP cc_start: 0.8199 (t0) cc_final: 0.7984 (t0) REVERT: D 335 LEU cc_start: 0.8389 (mm) cc_final: 0.7997 (tm) REVERT: D 586 ASP cc_start: 0.7774 (m-30) cc_final: 0.7492 (m-30) REVERT: D 979 ASP cc_start: 0.8286 (t70) cc_final: 0.7906 (t0) REVERT: G 342 PHE cc_start: 0.8525 (m-80) cc_final: 0.8227 (m-80) REVERT: G 351 TYR cc_start: 0.8072 (p90) cc_final: 0.7638 (p90) REVERT: G 429 PHE cc_start: 0.8254 (t80) cc_final: 0.7995 (t80) REVERT: G 624 ILE cc_start: 0.8433 (pt) cc_final: 0.8115 (pp) REVERT: G 979 ASP cc_start: 0.8324 (t70) cc_final: 0.7964 (t0) outliers start: 20 outliers final: 8 residues processed: 136 average time/residue: 1.2092 time to fit residues: 194.7539 Evaluate side-chains 123 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 258 TRP 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 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 249 optimal weight: 0.9980 chunk 216 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 290 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 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 = 0.3908 r_free = 0.3908 target = 0.123021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.071447 restraints weight = 48744.291| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.01 r_work: 0.2838 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1200 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= 0.141 Angle : 0.531 8.410 34917 Z= 0.277 Chirality : 0.045 0.217 4080 Planarity : 0.004 0.098 4416 Dihedral : 6.626 59.644 4329 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.81 % Allowed : 10.58 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3051 helix: 2.64 (0.22), residues: 612 sheet: 1.07 (0.20), residues: 663 loop : -1.10 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.004 0.001 HIS G1064 PHE 0.024 0.001 PHE G 133 TYR 0.017 0.001 TYR D1067 ARG 0.011 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 42) link_NAG-ASN : angle 1.78341 ( 126) link_BETA1-4 : bond 0.00312 ( 6) link_BETA1-4 : angle 0.79151 ( 18) hydrogen bonds : bond 0.05294 ( 939) hydrogen bonds : angle 4.70977 ( 2574) SS BOND : bond 0.00192 ( 39) SS BOND : angle 1.13812 ( 78) covalent geometry : bond 0.00337 (25494) covalent geometry : angle 0.51867 (34695) Misc. bond : bond 0.00651 ( 3) *********************** 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 146 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7912 (p90) cc_final: 0.7482 (p90) REVERT: A 624 ILE cc_start: 0.8373 (pt) cc_final: 0.7991 (pp) REVERT: A 979 ASP cc_start: 0.8327 (t70) cc_final: 0.7842 (OUTLIER) REVERT: A 988 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8610 (tm-30) REVERT: D 53 ASP cc_start: 0.8240 (t0) cc_final: 0.8008 (t0) REVERT: D 335 LEU cc_start: 0.8391 (mm) cc_final: 0.8007 (tm) REVERT: D 586 ASP cc_start: 0.7778 (m-30) cc_final: 0.7492 (m-30) REVERT: D 979 ASP cc_start: 0.8350 (t70) cc_final: 0.8075 (t0) REVERT: G 342 PHE cc_start: 0.8533 (m-80) cc_final: 0.8233 (m-80) REVERT: G 351 TYR cc_start: 0.8074 (p90) cc_final: 0.7639 (p90) REVERT: G 429 PHE cc_start: 0.8254 (t80) cc_final: 0.7972 (t80) REVERT: G 624 ILE cc_start: 0.8392 (pt) cc_final: 0.8070 (pp) REVERT: G 979 ASP cc_start: 0.8346 (t70) cc_final: 0.8001 (t0) outliers start: 22 outliers final: 10 residues processed: 140 average time/residue: 1.2314 time to fit residues: 205.7483 Evaluate side-chains 126 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 3.218 ------------------------------------------------------------------------------- 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 211 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 278 optimal weight: 0.1980 chunk 180 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN D 409 GLN G 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.123660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072185 restraints weight = 48380.207| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.00 r_work: 0.2855 rms_B_bonded: 3.04 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: 0.8594 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25584 Z= 0.117 Angle : 0.569 21.402 34917 Z= 0.291 Chirality : 0.044 0.212 4080 Planarity : 0.004 0.095 4416 Dihedral : 7.399 177.568 4329 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.81 % Allowed : 11.03 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3051 helix: 2.68 (0.22), residues: 612 sheet: 1.03 (0.20), residues: 669 loop : -1.07 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.002 0.000 HIS G1064 PHE 0.026 0.001 PHE D 342 TYR 0.016 0.001 TYR D1067 ARG 0.010 0.000 ARG G 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 42) link_NAG-ASN : angle 1.77210 ( 126) link_BETA1-4 : bond 0.00307 ( 6) link_BETA1-4 : angle 0.80054 ( 18) hydrogen bonds : bond 0.04916 ( 939) hydrogen bonds : angle 4.68139 ( 2574) SS BOND : bond 0.00172 ( 39) SS BOND : angle 1.03605 ( 78) covalent geometry : bond 0.00266 (25494) covalent geometry : angle 0.55785 (34695) Misc. bond : bond 0.01244 ( 3) *********************** 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 149 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7896 (p90) cc_final: 0.7474 (p90) REVERT: A 624 ILE cc_start: 0.8344 (pt) cc_final: 0.7962 (pp) REVERT: A 979 ASP cc_start: 0.8458 (t70) cc_final: 0.8029 (t0) REVERT: A 988 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8556 (tm-30) REVERT: D 53 ASP cc_start: 0.8239 (t0) cc_final: 0.8011 (t0) REVERT: D 335 LEU cc_start: 0.8392 (mm) cc_final: 0.8020 (tm) REVERT: D 586 ASP cc_start: 0.7740 (m-30) cc_final: 0.7460 (m-30) REVERT: D 979 ASP cc_start: 0.8357 (t70) cc_final: 0.8009 (t0) REVERT: G 342 PHE cc_start: 0.8527 (m-80) cc_final: 0.8253 (m-80) REVERT: G 351 TYR cc_start: 0.8071 (p90) cc_final: 0.7630 (p90) REVERT: G 429 PHE cc_start: 0.8287 (t80) cc_final: 0.8051 (t80) REVERT: G 624 ILE cc_start: 0.8406 (pt) cc_final: 0.8099 (pp) REVERT: G 979 ASP cc_start: 0.8468 (t70) cc_final: 0.8260 (t0) outliers start: 22 outliers final: 12 residues processed: 142 average time/residue: 1.2166 time to fit residues: 204.8212 Evaluate side-chains 132 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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 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 780 GLU 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 4 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 48 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.122703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070906 restraints weight = 48722.050| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.02 r_work: 0.2821 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25584 Z= 0.169 Angle : 0.608 28.467 34917 Z= 0.309 Chirality : 0.046 0.289 4080 Planarity : 0.008 0.440 4416 Dihedral : 7.478 171.594 4329 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.85 % Allowed : 11.28 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3051 helix: 2.48 (0.21), residues: 621 sheet: 1.01 (0.20), residues: 666 loop : -1.10 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.004 0.001 HIS G1064 PHE 0.026 0.001 PHE D 342 TYR 0.018 0.001 TYR D1067 ARG 0.037 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 42) link_NAG-ASN : angle 1.78187 ( 126) link_BETA1-4 : bond 0.00236 ( 6) link_BETA1-4 : angle 0.88447 ( 18) hydrogen bonds : bond 0.05600 ( 939) hydrogen bonds : angle 4.75775 ( 2574) SS BOND : bond 0.00192 ( 39) SS BOND : angle 1.22547 ( 78) covalent geometry : bond 0.00407 (25494) covalent geometry : angle 0.59739 (34695) Misc. bond : bond 0.01075 ( 3) *********************** 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 151 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7916 (p90) cc_final: 0.7493 (p90) REVERT: A 624 ILE cc_start: 0.8386 (pt) cc_final: 0.7987 (pp) REVERT: A 979 ASP cc_start: 0.8390 (t70) cc_final: 0.8030 (t0) REVERT: A 988 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8668 (tm-30) REVERT: D 53 ASP cc_start: 0.8234 (t0) cc_final: 0.8026 (t0) REVERT: D 335 LEU cc_start: 0.8412 (mm) cc_final: 0.8044 (tm) REVERT: D 586 ASP cc_start: 0.7799 (m-30) cc_final: 0.7442 (m-30) REVERT: D 624 ILE cc_start: 0.8410 (pt) cc_final: 0.7886 (pt) REVERT: D 979 ASP cc_start: 0.8385 (t70) cc_final: 0.8122 (t0) REVERT: G 342 PHE cc_start: 0.8527 (m-80) cc_final: 0.8291 (m-80) REVERT: G 351 TYR cc_start: 0.8082 (p90) cc_final: 0.7642 (p90) REVERT: G 429 PHE cc_start: 0.8232 (t80) cc_final: 0.7919 (t80) REVERT: G 624 ILE cc_start: 0.8391 (pt) cc_final: 0.8074 (pp) REVERT: G 979 ASP cc_start: 0.8625 (t70) cc_final: 0.8255 (t0) outliers start: 23 outliers final: 14 residues processed: 144 average time/residue: 1.4565 time to fit residues: 251.4680 Evaluate side-chains 132 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 3.142 ------------------------------------------------------------------------------- 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 895 GLN 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 258 TRP 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 D residue 1096 VAL Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 916 LEU 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 165 optimal weight: 0.0980 chunk 46 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 279 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.123980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072610 restraints weight = 48414.030| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.98 r_work: 0.2859 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 25584 Z= 0.115 Angle : 0.578 31.727 34917 Z= 0.293 Chirality : 0.044 0.267 4080 Planarity : 0.008 0.440 4416 Dihedral : 6.658 165.439 4329 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.96 % Allowed : 11.47 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3051 helix: 2.66 (0.22), residues: 612 sheet: 1.02 (0.20), residues: 669 loop : -1.05 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 64 HIS 0.002 0.000 HIS G1064 PHE 0.025 0.001 PHE D 342 TYR 0.016 0.001 TYR D1067 ARG 0.029 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 42) link_NAG-ASN : angle 1.77341 ( 126) link_BETA1-4 : bond 0.00357 ( 6) link_BETA1-4 : angle 0.73641 ( 18) hydrogen bonds : bond 0.04809 ( 939) hydrogen bonds : angle 4.70403 ( 2574) SS BOND : bond 0.00180 ( 39) SS BOND : angle 0.99869 ( 78) covalent geometry : bond 0.00256 (25494) covalent geometry : angle 0.56766 (34695) Misc. bond : bond 0.01300 ( 3) *********************** 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 154 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8344 (pt) cc_final: 0.7919 (pp) REVERT: A 979 ASP cc_start: 0.8295 (t70) cc_final: 0.7985 (OUTLIER) REVERT: A 988 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8578 (tm-30) REVERT: D 335 LEU cc_start: 0.8401 (mm) cc_final: 0.8038 (tm) REVERT: D 586 ASP cc_start: 0.7740 (m-30) cc_final: 0.7459 (m-30) REVERT: D 979 ASP cc_start: 0.8450 (t70) cc_final: 0.8013 (t0) REVERT: G 342 PHE cc_start: 0.8522 (m-80) cc_final: 0.8283 (m-80) REVERT: G 351 TYR cc_start: 0.8059 (p90) cc_final: 0.7598 (p90) REVERT: G 367 VAL cc_start: 0.8326 (m) cc_final: 0.8076 (p) REVERT: G 429 PHE cc_start: 0.8268 (t80) cc_final: 0.7939 (t80) REVERT: G 624 ILE cc_start: 0.8362 (pt) cc_final: 0.8017 (pp) REVERT: G 979 ASP cc_start: 0.8521 (t70) cc_final: 0.8244 (t0) REVERT: G 1092 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8472 (pm20) outliers start: 26 outliers final: 11 residues processed: 148 average time/residue: 1.8557 time to fit residues: 331.5599 Evaluate side-chains 129 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 649 CYS 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 1092 GLU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 165 optimal weight: 2.9990 chunk 127 optimal weight: 0.0270 chunk 208 optimal weight: 0.0060 chunk 74 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 289 optimal weight: 0.1980 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073371 restraints weight = 48520.185| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.01 r_work: 0.2885 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25584 Z= 0.099 Angle : 0.540 14.050 34917 Z= 0.277 Chirality : 0.043 0.222 4080 Planarity : 0.004 0.120 4416 Dihedral : 5.873 56.657 4329 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.74 % Allowed : 12.24 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3051 helix: 2.76 (0.22), residues: 612 sheet: 1.09 (0.20), residues: 663 loop : -0.99 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.002 0.000 HIS G 66 PHE 0.026 0.001 PHE G 133 TYR 0.015 0.001 TYR D1067 ARG 0.033 0.000 ARG G 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 42) link_NAG-ASN : angle 1.71851 ( 126) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 0.80124 ( 18) hydrogen bonds : bond 0.04351 ( 939) hydrogen bonds : angle 4.65002 ( 2574) SS BOND : bond 0.00201 ( 39) SS BOND : angle 0.92398 ( 78) covalent geometry : bond 0.00209 (25494) covalent geometry : angle 0.52949 (34695) Misc. bond : bond 0.00551 ( 3) *********************** 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 141 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 VAL cc_start: 0.8321 (m) cc_final: 0.8095 (p) REVERT: A 900 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8896 (mtm) REVERT: A 979 ASP cc_start: 0.8380 (t70) cc_final: 0.7920 (OUTLIER) REVERT: A 988 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8610 (tm-30) REVERT: D 335 LEU cc_start: 0.8419 (mm) cc_final: 0.8050 (tm) REVERT: D 367 VAL cc_start: 0.8390 (m) cc_final: 0.8156 (p) REVERT: D 586 ASP cc_start: 0.7712 (m-30) cc_final: 0.7478 (m-30) REVERT: D 979 ASP cc_start: 0.8424 (t70) cc_final: 0.8124 (t0) REVERT: G 351 TYR cc_start: 0.8065 (p90) cc_final: 0.7604 (p90) REVERT: G 367 VAL cc_start: 0.8277 (m) cc_final: 0.8036 (p) REVERT: G 429 PHE cc_start: 0.8192 (t80) cc_final: 0.7879 (t80) outliers start: 20 outliers final: 11 residues processed: 133 average time/residue: 1.3832 time to fit residues: 215.7148 Evaluate side-chains 123 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 2.786 ------------------------------------------------------------------------------- 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 900 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 307 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 183 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 251 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 277 optimal weight: 0.0270 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN G 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.124857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.073576 restraints weight = 48476.849| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.01 r_work: 0.2881 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1637 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= 0.101 Angle : 0.568 20.018 34917 Z= 0.290 Chirality : 0.044 0.216 4080 Planarity : 0.005 0.174 4416 Dihedral : 5.781 56.522 4329 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.66 % Allowed : 12.39 % Favored : 86.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3051 helix: 2.76 (0.22), residues: 615 sheet: 1.06 (0.20), residues: 669 loop : -0.96 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.005 0.000 HIS G 625 PHE 0.026 0.001 PHE D 342 TYR 0.016 0.001 TYR D1067 ARG 0.028 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 42) link_NAG-ASN : angle 1.67458 ( 126) link_BETA1-4 : bond 0.00349 ( 6) link_BETA1-4 : angle 0.77726 ( 18) hydrogen bonds : bond 0.04293 ( 939) hydrogen bonds : angle 4.64624 ( 2574) SS BOND : bond 0.00191 ( 39) SS BOND : angle 0.93876 ( 78) covalent geometry : bond 0.00222 (25494) covalent geometry : angle 0.55837 (34695) Misc. bond : bond 0.00629 ( 3) ********************** 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 135 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 VAL cc_start: 0.8310 (m) cc_final: 0.8088 (p) REVERT: A 979 ASP cc_start: 0.8435 (t70) cc_final: 0.8028 (OUTLIER) REVERT: A 988 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8583 (tm-30) REVERT: D 367 VAL cc_start: 0.8390 (m) cc_final: 0.8156 (p) REVERT: D 586 ASP cc_start: 0.7706 (m-30) cc_final: 0.7486 (m-30) REVERT: D 979 ASP cc_start: 0.8391 (t70) cc_final: 0.8009 (t0) REVERT: G 351 TYR cc_start: 0.8034 (p90) cc_final: 0.7579 (p90) REVERT: G 367 VAL cc_start: 0.8265 (m) cc_final: 0.8038 (p) REVERT: G 429 PHE cc_start: 0.8157 (t80) cc_final: 0.7839 (t80) outliers start: 18 outliers final: 9 residues processed: 128 average time/residue: 1.2801 time to fit residues: 196.0214 Evaluate side-chains 120 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 780 GLU 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 G residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 12 optimal weight: 8.9990 chunk 237 optimal weight: 0.7980 chunk 285 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 171 optimal weight: 0.0010 chunk 286 optimal weight: 0.3980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.125494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074477 restraints weight = 48531.325| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.98 r_work: 0.2902 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25584 Z= 0.098 Angle : 0.570 25.886 34917 Z= 0.288 Chirality : 0.044 0.218 4080 Planarity : 0.005 0.180 4416 Dihedral : 6.620 162.313 4329 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.48 % Allowed : 12.72 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3051 helix: 2.83 (0.22), residues: 612 sheet: 1.09 (0.20), residues: 669 loop : -0.94 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.001 0.000 HIS G 66 PHE 0.026 0.001 PHE A 133 TYR 0.015 0.001 TYR D1067 ARG 0.030 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 42) link_NAG-ASN : angle 1.65622 ( 126) link_BETA1-4 : bond 0.00324 ( 6) link_BETA1-4 : angle 0.76220 ( 18) hydrogen bonds : bond 0.04029 ( 939) hydrogen bonds : angle 4.58755 ( 2574) SS BOND : bond 0.00235 ( 39) SS BOND : angle 0.86659 ( 78) covalent geometry : bond 0.00204 (25494) covalent geometry : angle 0.56103 (34695) Misc. bond : bond 0.01144 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24125.55 seconds wall clock time: 425 minutes 47.98 seconds (25547.98 seconds total)