Starting phenix.real_space_refine on Thu Mar 5 23:20:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zss_14947/03_2026/7zss_14947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zss_14947/03_2026/7zss_14947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zss_14947/03_2026/7zss_14947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zss_14947/03_2026/7zss_14947.map" model { file = "/net/cci-nas-00/data/ceres_data/7zss_14947/03_2026/7zss_14947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zss_14947/03_2026/7zss_14947.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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 16533 2.51 5 N 4276 2.21 5 O 5025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25942 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7879 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 50, 'TRANS': 959} Chain breaks: 8 Chain: "B" Number of atoms: 7935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7935 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} Chain breaks: 8 Chain: "C" Number of atoms: 7927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7927 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 51, 'TRANS': 963} Chain breaks: 8 Chain: "D" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "P" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "h" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.41, per 1000 atoms: 0.25 Number of scatterers: 25942 At special positions: 0 Unit cell: (140.8, 216.32, 148.48, 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 5025 8.00 N 4276 7.00 C 16533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A1098 " " NAG A1203 " - " ASN A1134 " " NAG A1204 " - " ASN A 801 " " NAG A1205 " - " ASN A1074 " " NAG A1206 " - " ASN A 331 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 125 " " NAG A1209 " - " ASN A 164 " " NAG A1210 " - " ASN A 657 " " NAG A1211 " - " ASN A 282 " " NAG B1201 " - " ASN B1134 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 801 " " NAG B1205 " - " ASN B1098 " " NAG B1206 " - " ASN B 125 " " NAG B1207 " - " ASN B 164 " " NAG B1208 " - " ASN B 282 " " NAG B1209 " - " ASN B 331 " " NAG B1210 " - " ASN B 343 " " NAG B1211 " - " ASN B 657 " " NAG B1212 " - " ASN B 616 " " NAG B1213 " - " ASN B 603 " " NAG C1201 " - " ASN C 709 " " NAG C1202 " - " ASN C 282 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 122 " " NAG C1205 " - " ASN C 343 " " NAG C1206 " - " ASN C 331 " " NAG C1207 " - " ASN C 603 " " NAG C1208 " - " ASN C 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN C1134 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C1074 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C 717 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6046 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 45 sheets defined 27.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.740A pdb=" N ILE A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 411' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 742 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: 3.784A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.794A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.280A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.872A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.598A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.867A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.690A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.893A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.571A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.792A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.635A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.627A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.252A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.770A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.581A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.021A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.727A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.656A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.572A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 removed outlier: 3.538A pdb=" N SER C 637 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.950A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.634A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.804A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.347A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.569A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.792A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 24 removed outlier: 4.159A pdb=" N ALA D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE D 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 50 removed outlier: 3.968A pdb=" N ALA D 30 " --> pdb=" O ASN D 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 32 " --> pdb=" O GLY D 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 25 removed outlier: 3.638A pdb=" N ALA P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN P 12 " --> pdb=" O GLN P 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 50 removed outlier: 4.126A pdb=" N ALA P 30 " --> pdb=" O ASN P 26 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG P 31 " --> pdb=" O SER P 27 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 25 removed outlier: 3.826A pdb=" N GLN h 12 " --> pdb=" O GLN h 8 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE h 13 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR h 14 " --> pdb=" O ARG h 10 " (cutoff:3.500A) Processing helix chain 'h' and resid 27 through 50 removed outlier: 3.988A pdb=" N ARG h 32 " --> pdb=" O GLY h 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.133A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.638A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.809A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.649A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.542A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.548A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.672A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.599A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 7.099A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.596A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.596A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.434A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.018A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.520A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.906A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.949A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE B 515 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.502A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.122A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.567A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.446A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.601A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.626A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.602A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE1, first strand: chain 'C' and resid 313 through 319 removed outlier: 5.640A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.787A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.566A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.381A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.566A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.566A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.482A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1013 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 2.99 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: 8273 1.34 - 1.46: 6545 1.46 - 1.59: 11563 1.59 - 1.71: 2 1.71 - 1.83: 135 Bond restraints: 26518 Sorted by residual: bond pdb=" CG PRO A 812 " pdb=" CD PRO A 812 " ideal model delta sigma weight residual 1.503 1.371 0.132 3.40e-02 8.65e+02 1.52e+01 bond pdb=" CB PRO B 812 " pdb=" CG PRO B 812 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.11e+01 bond pdb=" CB PRO A 812 " pdb=" CG PRO A 812 " ideal model delta sigma weight residual 1.492 1.649 -0.157 5.00e-02 4.00e+02 9.82e+00 bond pdb=" CG PRO B 812 " pdb=" CD PRO B 812 " ideal model delta sigma weight residual 1.503 1.405 0.098 3.40e-02 8.65e+02 8.28e+00 bond pdb=" N HIS B 519 " pdb=" CA HIS B 519 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.42e-02 4.96e+03 6.51e+00 ... (remaining 26513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 35877 3.25 - 6.51: 162 6.51 - 9.76: 19 9.76 - 13.01: 4 13.01 - 16.27: 1 Bond angle restraints: 36063 Sorted by residual: angle pdb=" CA PRO B 812 " pdb=" N PRO B 812 " pdb=" CD PRO B 812 " ideal model delta sigma weight residual 112.00 95.73 16.27 1.40e+00 5.10e-01 1.35e+02 angle pdb=" CA PRO A 812 " pdb=" N PRO A 812 " pdb=" CD PRO A 812 " ideal model delta sigma weight residual 112.00 102.48 9.52 1.40e+00 5.10e-01 4.63e+01 angle pdb=" N PRO A 812 " pdb=" CD PRO A 812 " pdb=" CG PRO A 812 " ideal model delta sigma weight residual 103.20 93.33 9.87 1.50e+00 4.44e-01 4.33e+01 angle pdb=" N PRO B 812 " pdb=" CD PRO B 812 " pdb=" CG PRO B 812 " ideal model delta sigma weight residual 103.20 94.25 8.95 1.50e+00 4.44e-01 3.56e+01 angle pdb=" C PRO C 384 " pdb=" N THR C 385 " pdb=" CA THR C 385 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 ... (remaining 36058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 15394 23.18 - 46.35: 827 46.35 - 69.53: 101 69.53 - 92.70: 34 92.70 - 115.88: 38 Dihedral angle restraints: 16394 sinusoidal: 6995 harmonic: 9399 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.41 88.41 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.56 87.56 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -167.23 81.23 1 1.00e+01 1.00e-02 8.14e+01 ... (remaining 16391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3829 0.086 - 0.171: 369 0.171 - 0.257: 7 0.257 - 0.343: 3 0.343 - 0.428: 4 Chirality restraints: 4212 Sorted by residual: chirality pdb=" CB THR B 385 " pdb=" CA THR B 385 " pdb=" OG1 THR B 385 " pdb=" CG2 THR B 385 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB THR C 385 " pdb=" CA THR C 385 " pdb=" OG1 THR C 385 " pdb=" CG2 THR C 385 " both_signs ideal model delta sigma weight residual False 2.55 2.13 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CB THR A 385 " pdb=" CA THR A 385 " pdb=" OG1 THR A 385 " pdb=" CG2 THR A 385 " both_signs ideal model delta sigma weight residual False 2.55 2.13 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 4209 not shown) Planarity restraints: 4653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.099 5.00e-02 4.00e+02 1.47e-01 3.47e+01 pdb=" N PRO C 521 " -0.255 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " 0.087 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO B 812 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 518 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU C 518 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU C 518 " 0.024 2.00e-02 2.50e+03 pdb=" N HIS C 519 " 0.021 2.00e-02 2.50e+03 ... (remaining 4650 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 488 2.68 - 3.24: 24734 3.24 - 3.79: 38150 3.79 - 4.35: 51220 4.35 - 4.90: 84971 Nonbonded interactions: 199563 Sorted by model distance: nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 2.130 3.120 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.152 3.040 nonbonded pdb=" OG SER B 443 " pdb=" O PHE B 497 " model vdw 2.192 3.040 nonbonded pdb=" O TYR B 495 " pdb=" OH TYR B 505 " model vdw 2.192 3.040 nonbonded pdb=" OE1 GLU h 24 " pdb=" ND2 ASN h 26 " model vdw 2.193 3.120 ... (remaining 199558 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' and resid 27 through 1208) selection = (chain 'B' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1208)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1208)) } ncs_group { reference = chain 'D' selection = chain 'P' selection = chain 'h' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.080 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 0.166 26600 Z= 0.196 Angle : 0.720 19.699 36272 Z= 0.391 Chirality : 0.047 0.428 4212 Planarity : 0.005 0.147 4615 Dihedral : 14.996 115.881 10237 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.45 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3176 helix: 1.91 (0.19), residues: 790 sheet: 0.16 (0.20), residues: 698 loop : -1.79 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG h 35 TYR 0.024 0.001 TYR h 14 PHE 0.028 0.001 PHE D 33 TRP 0.016 0.001 TRP A 886 HIS 0.010 0.001 HIS P 15 Details of bonding type rmsd covalent geometry : bond 0.00426 (26518) covalent geometry : angle 0.69819 (36063) SS BOND : bond 0.00400 ( 37) SS BOND : angle 1.32858 ( 74) hydrogen bonds : bond 0.19305 ( 989) hydrogen bonds : angle 7.74564 ( 2850) link_BETA1-4 : bond 0.00568 ( 7) link_BETA1-4 : angle 1.07664 ( 21) link_NAG-ASN : bond 0.00619 ( 38) link_NAG-ASN : angle 3.09392 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7368 (tm130) REVERT: A 81 ASN cc_start: 0.6548 (m-40) cc_final: 0.6106 (p0) REVERT: A 129 LYS cc_start: 0.5762 (mttp) cc_final: 0.5206 (tptm) REVERT: A 168 PHE cc_start: 0.7017 (t80) cc_final: 0.6482 (t80) REVERT: A 190 ARG cc_start: 0.6612 (mtt90) cc_final: 0.6008 (mmt-90) REVERT: A 574 ASP cc_start: 0.7074 (m-30) cc_final: 0.6863 (m-30) REVERT: A 869 MET cc_start: 0.8776 (mtt) cc_final: 0.8478 (mtt) REVERT: B 130 VAL cc_start: 0.6099 (p) cc_final: 0.5884 (t) REVERT: B 202 LYS cc_start: 0.7867 (mttp) cc_final: 0.7517 (mtmm) REVERT: B 342 PHE cc_start: 0.7949 (m-80) cc_final: 0.7600 (m-80) REVERT: B 440 ASN cc_start: 0.7878 (m-40) cc_final: 0.7649 (p0) REVERT: B 564 GLN cc_start: 0.6403 (tm-30) cc_final: 0.5915 (tm-30) REVERT: C 201 PHE cc_start: 0.5644 (m-80) cc_final: 0.4734 (t80) REVERT: C 202 LYS cc_start: 0.6912 (mtpt) cc_final: 0.6572 (mtmm) REVERT: C 380 TYR cc_start: 0.7922 (m-80) cc_final: 0.7645 (m-10) REVERT: C 420 ASP cc_start: 0.6066 (m-30) cc_final: 0.5745 (t0) REVERT: C 495 TYR cc_start: 0.6271 (m-80) cc_final: 0.5904 (m-80) REVERT: C 900 MET cc_start: 0.8745 (mtp) cc_final: 0.8426 (mtm) REVERT: P 3 MET cc_start: 0.4714 (tpp) cc_final: 0.3205 (tmt) REVERT: P 36 ILE cc_start: 0.6651 (mp) cc_final: 0.6326 (mp) REVERT: h 17 GLN cc_start: 0.6138 (pt0) cc_final: 0.5744 (pt0) REVERT: h 33 PHE cc_start: 0.6442 (m-10) cc_final: 0.6221 (m-10) REVERT: h 47 TYR cc_start: 0.4556 (t80) cc_final: 0.3889 (t80) outliers start: 0 outliers final: 1 residues processed: 302 average time/residue: 0.5662 time to fit residues: 203.2086 Evaluate side-chains 161 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 440 ASN A 544 ASN A 914 ASN B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 196 ASN C 207 HIS C 703 ASN C1011 GLN P 12 GLN P 15 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.181146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112085 restraints weight = 38564.059| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.36 r_work: 0.3360 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26600 Z= 0.129 Angle : 0.636 19.261 36272 Z= 0.318 Chirality : 0.047 0.385 4212 Planarity : 0.005 0.100 4615 Dihedral : 10.316 106.515 4434 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.26 % Favored : 94.55 % Rotamer: Outliers : 1.00 % Allowed : 6.68 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3176 helix: 2.25 (0.19), residues: 789 sheet: 0.28 (0.20), residues: 700 loop : -1.70 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 102 TYR 0.022 0.001 TYR B1067 PHE 0.020 0.001 PHE C 377 TRP 0.014 0.001 TRP B 436 HIS 0.011 0.001 HIS P 15 Details of bonding type rmsd covalent geometry : bond 0.00290 (26518) covalent geometry : angle 0.61110 (36063) SS BOND : bond 0.00480 ( 37) SS BOND : angle 1.47431 ( 74) hydrogen bonds : bond 0.04942 ( 989) hydrogen bonds : angle 5.78020 ( 2850) link_BETA1-4 : bond 0.00592 ( 7) link_BETA1-4 : angle 1.06073 ( 21) link_NAG-ASN : bond 0.00671 ( 38) link_NAG-ASN : angle 2.98399 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7140 (tm130) REVERT: A 81 ASN cc_start: 0.6951 (m-40) cc_final: 0.6370 (p0) REVERT: A 129 LYS cc_start: 0.5187 (mttp) cc_final: 0.4646 (tptm) REVERT: A 168 PHE cc_start: 0.7207 (t80) cc_final: 0.6476 (t80) REVERT: A 190 ARG cc_start: 0.6670 (mtt90) cc_final: 0.6214 (mmt-90) REVERT: A 207 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6815 (t70) REVERT: A 396 TYR cc_start: 0.5556 (m-10) cc_final: 0.5204 (m-80) REVERT: A 564 GLN cc_start: 0.7743 (mm110) cc_final: 0.7518 (mm110) REVERT: A 574 ASP cc_start: 0.7433 (m-30) cc_final: 0.6959 (m-30) REVERT: A 702 GLU cc_start: 0.8349 (pt0) cc_final: 0.7997 (tt0) REVERT: A 869 MET cc_start: 0.8963 (mtt) cc_final: 0.8666 (mtt) REVERT: B 188 ASN cc_start: 0.6939 (m-40) cc_final: 0.6430 (p0) REVERT: B 202 LYS cc_start: 0.7462 (mttp) cc_final: 0.7260 (mtpp) REVERT: B 342 PHE cc_start: 0.7864 (m-80) cc_final: 0.7534 (m-80) REVERT: B 440 ASN cc_start: 0.8003 (m-40) cc_final: 0.7646 (p0) REVERT: B 564 GLN cc_start: 0.5803 (tm-30) cc_final: 0.5016 (tm-30) REVERT: C 194 PHE cc_start: 0.5940 (m-10) cc_final: 0.5606 (m-10) REVERT: C 196 ASN cc_start: 0.5236 (OUTLIER) cc_final: 0.5013 (t0) REVERT: C 201 PHE cc_start: 0.4944 (m-80) cc_final: 0.4187 (t80) REVERT: C 202 LYS cc_start: 0.6805 (mtpt) cc_final: 0.6425 (mptt) REVERT: C 380 TYR cc_start: 0.7769 (m-80) cc_final: 0.7438 (m-10) REVERT: C 420 ASP cc_start: 0.6567 (m-30) cc_final: 0.6231 (t0) REVERT: C 495 TYR cc_start: 0.6176 (m-80) cc_final: 0.5589 (m-80) REVERT: C 515 PHE cc_start: 0.6404 (m-10) cc_final: 0.6196 (m-80) REVERT: C 735 SER cc_start: 0.8891 (t) cc_final: 0.8571 (p) REVERT: C 868 GLU cc_start: 0.7965 (mp0) cc_final: 0.7579 (mt-10) REVERT: C 900 MET cc_start: 0.8940 (mtp) cc_final: 0.8637 (mtm) REVERT: C 1005 GLN cc_start: 0.8417 (mt0) cc_final: 0.8197 (mt0) REVERT: P 3 MET cc_start: 0.3676 (tpp) cc_final: 0.2889 (tmt) REVERT: P 33 PHE cc_start: 0.5958 (m-80) cc_final: 0.5570 (m-80) REVERT: h 17 GLN cc_start: 0.5302 (pt0) cc_final: 0.4971 (pt0) REVERT: h 39 GLN cc_start: 0.8487 (tp40) cc_final: 0.7917 (tm-30) REVERT: h 40 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.4941 (t80) REVERT: h 44 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3857 (pp) REVERT: h 47 TYR cc_start: 0.4273 (t80) cc_final: 0.3678 (t80) outliers start: 28 outliers final: 10 residues processed: 204 average time/residue: 0.5510 time to fit residues: 134.3409 Evaluate side-chains 167 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 TYR Chi-restraints excluded: chain h residue 44 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 96 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 241 optimal weight: 0.0030 chunk 213 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 544 ASN B 218 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 703 ASN C 914 ASN C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.178183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107735 restraints weight = 38432.940| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.37 r_work: 0.3293 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26600 Z= 0.171 Angle : 0.652 19.281 36272 Z= 0.325 Chirality : 0.048 0.426 4212 Planarity : 0.004 0.083 4615 Dihedral : 8.214 96.373 4434 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.73 % Favored : 94.08 % Rotamer: Outliers : 1.53 % Allowed : 9.49 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3176 helix: 2.02 (0.19), residues: 791 sheet: 0.18 (0.19), residues: 705 loop : -1.71 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 102 TYR 0.023 0.002 TYR B1067 PHE 0.021 0.002 PHE A 906 TRP 0.015 0.001 TRP B 436 HIS 0.017 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00418 (26518) covalent geometry : angle 0.62466 (36063) SS BOND : bond 0.00585 ( 37) SS BOND : angle 1.69269 ( 74) hydrogen bonds : bond 0.05365 ( 989) hydrogen bonds : angle 5.47686 ( 2850) link_BETA1-4 : bond 0.00420 ( 7) link_BETA1-4 : angle 1.23988 ( 21) link_NAG-ASN : bond 0.00640 ( 38) link_NAG-ASN : angle 3.10773 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7083 (tm130) REVERT: A 129 LYS cc_start: 0.5316 (mttp) cc_final: 0.5068 (tptm) REVERT: A 168 PHE cc_start: 0.7287 (t80) cc_final: 0.6471 (t80) REVERT: A 207 HIS cc_start: 0.7515 (m-70) cc_final: 0.7016 (t-90) REVERT: A 309 GLU cc_start: 0.7472 (pm20) cc_final: 0.7226 (pm20) REVERT: A 396 TYR cc_start: 0.5212 (m-10) cc_final: 0.4937 (m-80) REVERT: A 564 GLN cc_start: 0.7591 (mm110) cc_final: 0.7317 (mm110) REVERT: A 869 MET cc_start: 0.9062 (mtt) cc_final: 0.8814 (mtt) REVERT: A 964 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8006 (mmpt) REVERT: B 111 ASP cc_start: 0.4870 (t0) cc_final: 0.4426 (p0) REVERT: B 188 ASN cc_start: 0.6964 (m-40) cc_final: 0.6480 (p0) REVERT: B 202 LYS cc_start: 0.7593 (mttp) cc_final: 0.6852 (mtmm) REVERT: B 342 PHE cc_start: 0.7899 (m-80) cc_final: 0.7586 (m-80) REVERT: B 347 PHE cc_start: 0.4727 (m-10) cc_final: 0.4256 (m-10) REVERT: B 440 ASN cc_start: 0.8005 (m-40) cc_final: 0.7654 (p0) REVERT: B 564 GLN cc_start: 0.5872 (tm-30) cc_final: 0.4929 (tm-30) REVERT: C 201 PHE cc_start: 0.4742 (m-80) cc_final: 0.4108 (t80) REVERT: C 202 LYS cc_start: 0.6769 (mtpt) cc_final: 0.6345 (mptt) REVERT: C 420 ASP cc_start: 0.6715 (m-30) cc_final: 0.6391 (t0) REVERT: C 495 TYR cc_start: 0.6034 (m-80) cc_final: 0.5457 (m-80) REVERT: C 528 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7183 (mmmm) REVERT: C 868 GLU cc_start: 0.8096 (mp0) cc_final: 0.7771 (mt-10) REVERT: C 900 MET cc_start: 0.9011 (mtp) cc_final: 0.8700 (mtm) REVERT: P 3 MET cc_start: 0.3965 (tpp) cc_final: 0.3189 (tmt) REVERT: P 33 PHE cc_start: 0.6076 (m-80) cc_final: 0.5700 (m-80) REVERT: P 36 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6987 (mt) REVERT: h 17 GLN cc_start: 0.5181 (pt0) cc_final: 0.4953 (pt0) REVERT: h 39 GLN cc_start: 0.8498 (tp40) cc_final: 0.7884 (tm-30) REVERT: h 40 TYR cc_start: 0.5730 (OUTLIER) cc_final: 0.5216 (t80) REVERT: h 44 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3742 (pp) outliers start: 43 outliers final: 20 residues processed: 193 average time/residue: 0.5572 time to fit residues: 128.7682 Evaluate side-chains 170 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 TYR Chi-restraints excluded: chain h residue 44 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 316 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 287 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 207 HIS A 440 ASN A 544 ASN A 613 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 703 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.175768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106231 restraints weight = 38037.380| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.62 r_work: 0.3240 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26600 Z= 0.203 Angle : 0.684 19.448 36272 Z= 0.342 Chirality : 0.050 0.387 4212 Planarity : 0.005 0.078 4615 Dihedral : 7.699 89.950 4434 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.08 % Favored : 93.73 % Rotamer: Outliers : 2.03 % Allowed : 11.41 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3176 helix: 1.74 (0.19), residues: 791 sheet: 0.10 (0.19), residues: 717 loop : -1.78 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 815 TYR 0.024 0.002 TYR B1067 PHE 0.023 0.002 PHE B 168 TRP 0.015 0.002 TRP B 436 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00495 (26518) covalent geometry : angle 0.65368 (36063) SS BOND : bond 0.00656 ( 37) SS BOND : angle 2.01551 ( 74) hydrogen bonds : bond 0.05818 ( 989) hydrogen bonds : angle 5.43201 ( 2850) link_BETA1-4 : bond 0.00497 ( 7) link_BETA1-4 : angle 1.26394 ( 21) link_NAG-ASN : bond 0.00662 ( 38) link_NAG-ASN : angle 3.27197 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7180 (tm130) REVERT: A 129 LYS cc_start: 0.5172 (mttp) cc_final: 0.4939 (tptm) REVERT: A 168 PHE cc_start: 0.7078 (t80) cc_final: 0.5941 (t80) REVERT: A 207 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6771 (t-90) REVERT: A 309 GLU cc_start: 0.7548 (pm20) cc_final: 0.7296 (pm20) REVERT: A 361 CYS cc_start: 0.1650 (OUTLIER) cc_final: 0.1135 (p) REVERT: A 396 TYR cc_start: 0.4880 (m-10) cc_final: 0.4625 (m-80) REVERT: A 646 ARG cc_start: 0.8328 (tpt170) cc_final: 0.8122 (mmt180) REVERT: A 869 MET cc_start: 0.9072 (mtt) cc_final: 0.8837 (mtt) REVERT: B 111 ASP cc_start: 0.4968 (t0) cc_final: 0.4532 (p0) REVERT: B 342 PHE cc_start: 0.7923 (m-80) cc_final: 0.7661 (m-80) REVERT: B 347 PHE cc_start: 0.4903 (m-10) cc_final: 0.4485 (m-10) REVERT: B 355 ARG cc_start: 0.7182 (ttm170) cc_final: 0.6669 (tpp-160) REVERT: B 440 ASN cc_start: 0.7995 (m-40) cc_final: 0.7642 (p0) REVERT: B 564 GLN cc_start: 0.5848 (tm-30) cc_final: 0.4898 (tm-30) REVERT: C 201 PHE cc_start: 0.4772 (m-80) cc_final: 0.4006 (t80) REVERT: C 202 LYS cc_start: 0.6809 (mtpt) cc_final: 0.6360 (mptt) REVERT: C 495 TYR cc_start: 0.5685 (m-80) cc_final: 0.5175 (m-80) REVERT: C 528 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7105 (mmmm) REVERT: C 540 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.6186 (p0) REVERT: C 995 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7440 (mtt180) REVERT: P 3 MET cc_start: 0.4025 (tpp) cc_final: 0.3291 (tmt) REVERT: P 33 PHE cc_start: 0.6142 (m-80) cc_final: 0.5775 (m-80) REVERT: P 36 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6913 (mt) REVERT: h 17 GLN cc_start: 0.5209 (pt0) cc_final: 0.4889 (pt0) REVERT: h 40 TYR cc_start: 0.5650 (OUTLIER) cc_final: 0.5333 (t80) REVERT: h 44 ILE cc_start: 0.4144 (OUTLIER) cc_final: 0.3827 (pp) outliers start: 57 outliers final: 31 residues processed: 207 average time/residue: 0.5224 time to fit residues: 130.2916 Evaluate side-chains 179 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 TYR Chi-restraints excluded: chain h residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 23 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 283 optimal weight: 0.3980 chunk 191 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 213 optimal weight: 20.0000 chunk 214 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 440 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1088 HIS C 703 ASN C 913 GLN h 15 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.176290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106321 restraints weight = 37994.504| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.33 r_work: 0.3267 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26600 Z= 0.160 Angle : 0.634 19.354 36272 Z= 0.317 Chirality : 0.047 0.383 4212 Planarity : 0.004 0.072 4615 Dihedral : 7.371 89.640 4434 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.82 % Favored : 93.99 % Rotamer: Outliers : 2.38 % Allowed : 12.58 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3176 helix: 1.85 (0.19), residues: 790 sheet: 0.11 (0.19), residues: 716 loop : -1.75 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.020 0.001 TYR B1067 PHE 0.023 0.002 PHE B 133 TRP 0.017 0.001 TRP B 436 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00386 (26518) covalent geometry : angle 0.60411 (36063) SS BOND : bond 0.00596 ( 37) SS BOND : angle 1.85059 ( 74) hydrogen bonds : bond 0.05279 ( 989) hydrogen bonds : angle 5.30291 ( 2850) link_BETA1-4 : bond 0.00394 ( 7) link_BETA1-4 : angle 1.16569 ( 21) link_NAG-ASN : bond 0.00625 ( 38) link_NAG-ASN : angle 3.18366 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 149 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7164 (tm130) REVERT: A 129 LYS cc_start: 0.5158 (mttp) cc_final: 0.4932 (tptm) REVERT: A 168 PHE cc_start: 0.7135 (t80) cc_final: 0.5875 (t80) REVERT: A 207 HIS cc_start: 0.7354 (OUTLIER) cc_final: 0.6979 (t70) REVERT: A 309 GLU cc_start: 0.7516 (pm20) cc_final: 0.7249 (pm20) REVERT: A 396 TYR cc_start: 0.4867 (m-10) cc_final: 0.4630 (m-80) REVERT: A 564 GLN cc_start: 0.7831 (mm110) cc_final: 0.7627 (mm-40) REVERT: A 646 ARG cc_start: 0.8312 (tpt170) cc_final: 0.8094 (mmt180) REVERT: A 670 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7645 (pt) REVERT: A 869 MET cc_start: 0.9027 (mtt) cc_final: 0.8758 (mtt) REVERT: B 111 ASP cc_start: 0.4967 (t0) cc_final: 0.4474 (p0) REVERT: B 342 PHE cc_start: 0.7910 (m-80) cc_final: 0.7694 (m-80) REVERT: B 347 PHE cc_start: 0.5100 (m-10) cc_final: 0.4733 (m-10) REVERT: B 434 ILE cc_start: 0.5320 (OUTLIER) cc_final: 0.4725 (mm) REVERT: B 440 ASN cc_start: 0.7996 (m-40) cc_final: 0.7639 (p0) REVERT: B 564 GLN cc_start: 0.5840 (tm-30) cc_final: 0.4848 (tm-30) REVERT: B 581 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7820 (p) REVERT: C 201 PHE cc_start: 0.4778 (m-80) cc_final: 0.4078 (t80) REVERT: C 202 LYS cc_start: 0.6835 (mtpt) cc_final: 0.6317 (mptt) REVERT: C 239 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.5833 (mt0) REVERT: C 495 TYR cc_start: 0.5673 (m-80) cc_final: 0.5142 (m-80) REVERT: C 528 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7121 (mmmm) REVERT: C 540 ASN cc_start: 0.6504 (OUTLIER) cc_final: 0.6248 (p0) REVERT: C 660 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6311 (p90) REVERT: C 671 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8326 (p) REVERT: C 995 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7470 (mtt180) REVERT: P 3 MET cc_start: 0.4044 (tpp) cc_final: 0.3784 (tpt) REVERT: P 33 PHE cc_start: 0.6374 (m-80) cc_final: 0.6011 (m-80) REVERT: P 36 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6901 (mt) REVERT: h 40 TYR cc_start: 0.5472 (OUTLIER) cc_final: 0.5263 (t80) REVERT: h 44 ILE cc_start: 0.4160 (OUTLIER) cc_final: 0.3847 (pp) outliers start: 67 outliers final: 38 residues processed: 200 average time/residue: 0.5175 time to fit residues: 125.2977 Evaluate side-chains 184 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 TYR Chi-restraints excluded: chain h residue 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 213 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 207 HIS A 440 ASN A 544 ASN A 901 GLN B 196 ASN B 774 GLN B1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.174596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.104520 restraints weight = 38291.688| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.34 r_work: 0.3245 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26600 Z= 0.218 Angle : 0.692 19.506 36272 Z= 0.346 Chirality : 0.050 0.385 4212 Planarity : 0.005 0.072 4615 Dihedral : 7.380 87.843 4434 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.27 % Favored : 93.55 % Rotamer: Outliers : 3.16 % Allowed : 13.01 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3176 helix: 1.66 (0.19), residues: 789 sheet: 0.00 (0.19), residues: 712 loop : -1.82 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 905 TYR 0.023 0.002 TYR B1067 PHE 0.026 0.002 PHE B 168 TRP 0.018 0.002 TRP B 436 HIS 0.025 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00539 (26518) covalent geometry : angle 0.66062 (36063) SS BOND : bond 0.00724 ( 37) SS BOND : angle 2.20083 ( 74) hydrogen bonds : bond 0.05990 ( 989) hydrogen bonds : angle 5.38731 ( 2850) link_BETA1-4 : bond 0.00371 ( 7) link_BETA1-4 : angle 1.26489 ( 21) link_NAG-ASN : bond 0.00622 ( 38) link_NAG-ASN : angle 3.28347 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 146 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7217 (tm130) REVERT: A 168 PHE cc_start: 0.7223 (t80) cc_final: 0.6013 (t80) REVERT: A 309 GLU cc_start: 0.7576 (pm20) cc_final: 0.7327 (pm20) REVERT: A 361 CYS cc_start: 0.1874 (OUTLIER) cc_final: 0.1336 (p) REVERT: A 396 TYR cc_start: 0.4879 (m-10) cc_final: 0.4642 (m-80) REVERT: A 646 ARG cc_start: 0.8359 (tpt170) cc_final: 0.8139 (mmt180) REVERT: A 670 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7735 (pt) REVERT: B 111 ASP cc_start: 0.4976 (t0) cc_final: 0.4435 (p0) REVERT: B 188 ASN cc_start: 0.6933 (m-40) cc_final: 0.6628 (p0) REVERT: B 271 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: B 342 PHE cc_start: 0.7909 (m-80) cc_final: 0.7671 (m-80) REVERT: B 347 PHE cc_start: 0.5683 (m-10) cc_final: 0.5381 (m-10) REVERT: B 355 ARG cc_start: 0.7170 (ttm170) cc_final: 0.6778 (tpp-160) REVERT: B 434 ILE cc_start: 0.5373 (OUTLIER) cc_final: 0.4814 (mm) REVERT: B 440 ASN cc_start: 0.8005 (m-40) cc_final: 0.7644 (p0) REVERT: B 581 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7725 (p) REVERT: B 641 ASN cc_start: 0.7442 (t0) cc_final: 0.7188 (p0) REVERT: C 201 PHE cc_start: 0.4786 (m-80) cc_final: 0.3961 (t80) REVERT: C 202 LYS cc_start: 0.6955 (mtpt) cc_final: 0.6481 (mptt) REVERT: C 239 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6445 (mt0) REVERT: C 495 TYR cc_start: 0.5756 (m-80) cc_final: 0.5399 (m-80) REVERT: C 528 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7254 (mmmm) REVERT: C 540 ASN cc_start: 0.6477 (OUTLIER) cc_final: 0.6226 (p0) REVERT: C 660 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6364 (p90) REVERT: C 671 CYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8366 (p) REVERT: C 740 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8077 (ttt) REVERT: C 995 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7530 (mtt180) REVERT: P 3 MET cc_start: 0.4092 (tpp) cc_final: 0.3802 (tpt) REVERT: P 33 PHE cc_start: 0.6231 (m-80) cc_final: 0.5839 (m-80) REVERT: P 36 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6904 (mt) REVERT: h 44 ILE cc_start: 0.4112 (OUTLIER) cc_final: 0.3815 (pp) outliers start: 89 outliers final: 48 residues processed: 219 average time/residue: 0.4808 time to fit residues: 128.4103 Evaluate side-chains 194 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 50 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 544 ASN A 901 GLN B1010 GLN C 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.175651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106539 restraints weight = 38197.507| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.33 r_work: 0.3258 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26600 Z= 0.165 Angle : 0.647 19.301 36272 Z= 0.321 Chirality : 0.048 0.424 4212 Planarity : 0.004 0.069 4615 Dihedral : 7.135 87.568 4434 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 2.99 % Allowed : 13.62 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3176 helix: 1.79 (0.19), residues: 790 sheet: 0.01 (0.19), residues: 710 loop : -1.77 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 408 TYR 0.020 0.001 TYR B1067 PHE 0.026 0.002 PHE B 133 TRP 0.021 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00397 (26518) covalent geometry : angle 0.61642 (36063) SS BOND : bond 0.00613 ( 37) SS BOND : angle 1.99983 ( 74) hydrogen bonds : bond 0.05287 ( 989) hydrogen bonds : angle 5.25412 ( 2850) link_BETA1-4 : bond 0.00403 ( 7) link_BETA1-4 : angle 1.14009 ( 21) link_NAG-ASN : bond 0.00604 ( 38) link_NAG-ASN : angle 3.19288 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 141 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7230 (tm130) REVERT: A 168 PHE cc_start: 0.7185 (t80) cc_final: 0.6107 (t80) REVERT: A 309 GLU cc_start: 0.7563 (pm20) cc_final: 0.7306 (pm20) REVERT: A 361 CYS cc_start: 0.1861 (OUTLIER) cc_final: 0.1339 (p) REVERT: A 440 ASN cc_start: 0.4898 (OUTLIER) cc_final: 0.4683 (p0) REVERT: A 646 ARG cc_start: 0.8364 (tpt170) cc_final: 0.8108 (mmt180) REVERT: A 670 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7756 (pt) REVERT: B 111 ASP cc_start: 0.4947 (t0) cc_final: 0.4407 (p0) REVERT: B 236 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7102 (p) REVERT: B 271 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: B 309 GLU cc_start: 0.7982 (mp0) cc_final: 0.7673 (mt-10) REVERT: B 342 PHE cc_start: 0.7902 (m-80) cc_final: 0.7687 (m-80) REVERT: B 347 PHE cc_start: 0.5795 (m-10) cc_final: 0.5565 (m-10) REVERT: B 355 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6930 (tpp-160) REVERT: B 434 ILE cc_start: 0.5413 (OUTLIER) cc_final: 0.4807 (mm) REVERT: B 440 ASN cc_start: 0.7964 (m-40) cc_final: 0.7579 (p0) REVERT: B 581 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7736 (p) REVERT: B 641 ASN cc_start: 0.7718 (t0) cc_final: 0.7294 (p0) REVERT: B 748 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: C 202 LYS cc_start: 0.6971 (mtpt) cc_final: 0.6565 (mptt) REVERT: C 239 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6478 (mt0) REVERT: C 495 TYR cc_start: 0.5749 (m-80) cc_final: 0.5396 (m-80) REVERT: C 528 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7273 (mmmm) REVERT: C 540 ASN cc_start: 0.6554 (OUTLIER) cc_final: 0.6294 (p0) REVERT: C 660 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.6398 (p90) REVERT: C 671 CYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8277 (p) REVERT: C 995 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7578 (mtt180) REVERT: P 3 MET cc_start: 0.4094 (tpp) cc_final: 0.3792 (tpt) REVERT: P 33 PHE cc_start: 0.6295 (m-80) cc_final: 0.5910 (m-80) REVERT: P 36 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6880 (mt) outliers start: 84 outliers final: 52 residues processed: 212 average time/residue: 0.4779 time to fit residues: 123.8574 Evaluate side-chains 196 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain h residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 199 optimal weight: 0.0060 chunk 226 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 308 optimal weight: 0.4980 chunk 159 optimal weight: 6.9990 chunk 241 optimal weight: 0.6980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN B1010 GLN C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.176669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108021 restraints weight = 38344.549| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.32 r_work: 0.3277 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26600 Z= 0.128 Angle : 0.616 19.206 36272 Z= 0.306 Chirality : 0.046 0.410 4212 Planarity : 0.004 0.069 4615 Dihedral : 6.886 86.831 4434 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 2.49 % Allowed : 14.26 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3176 helix: 1.98 (0.19), residues: 791 sheet: 0.09 (0.19), residues: 711 loop : -1.69 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.023 0.001 TYR C 170 PHE 0.026 0.001 PHE B 168 TRP 0.023 0.001 TRP B 436 HIS 0.003 0.001 HIS h 15 Details of bonding type rmsd covalent geometry : bond 0.00296 (26518) covalent geometry : angle 0.58624 (36063) SS BOND : bond 0.00624 ( 37) SS BOND : angle 1.76681 ( 74) hydrogen bonds : bond 0.04759 ( 989) hydrogen bonds : angle 5.13779 ( 2850) link_BETA1-4 : bond 0.00444 ( 7) link_BETA1-4 : angle 1.10087 ( 21) link_NAG-ASN : bond 0.00603 ( 38) link_NAG-ASN : angle 3.10564 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 146 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7144 (tm130) REVERT: A 168 PHE cc_start: 0.7159 (t80) cc_final: 0.6095 (t80) REVERT: A 309 GLU cc_start: 0.7537 (pm20) cc_final: 0.7272 (pm20) REVERT: A 361 CYS cc_start: 0.1758 (OUTLIER) cc_final: 0.0860 (p) REVERT: A 564 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7474 (mm-40) REVERT: A 581 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7542 (p) REVERT: A 646 ARG cc_start: 0.8293 (tpt170) cc_final: 0.8026 (mmt180) REVERT: A 869 MET cc_start: 0.8984 (mtt) cc_final: 0.8756 (mtt) REVERT: B 111 ASP cc_start: 0.4909 (t0) cc_final: 0.4343 (p0) REVERT: B 188 ASN cc_start: 0.6861 (m-40) cc_final: 0.6577 (p0) REVERT: B 236 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.7027 (p) REVERT: B 271 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: B 342 PHE cc_start: 0.7872 (m-80) cc_final: 0.7615 (m-80) REVERT: B 347 PHE cc_start: 0.5844 (m-10) cc_final: 0.5542 (m-10) REVERT: B 357 ARG cc_start: 0.6236 (tpp80) cc_final: 0.5881 (tpp80) REVERT: B 434 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.5026 (mt) REVERT: B 440 ASN cc_start: 0.7843 (m-40) cc_final: 0.7516 (p0) REVERT: B 581 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7697 (p) REVERT: B 641 ASN cc_start: 0.7676 (t0) cc_final: 0.7157 (p0) REVERT: C 190 ARG cc_start: 0.5673 (mmt90) cc_final: 0.5160 (mmm-85) REVERT: C 202 LYS cc_start: 0.6926 (mtpt) cc_final: 0.6531 (mptt) REVERT: C 420 ASP cc_start: 0.6779 (t0) cc_final: 0.6424 (t0) REVERT: C 495 TYR cc_start: 0.5756 (m-80) cc_final: 0.5286 (m-80) REVERT: C 528 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7249 (mmmm) REVERT: C 540 ASN cc_start: 0.6484 (OUTLIER) cc_final: 0.6230 (p0) REVERT: C 660 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.6140 (p90) REVERT: C 671 CYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8288 (p) REVERT: C 995 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7503 (mtt180) REVERT: P 3 MET cc_start: 0.4079 (tpp) cc_final: 0.3780 (tpt) REVERT: P 33 PHE cc_start: 0.6316 (m-80) cc_final: 0.6003 (m-80) REVERT: P 36 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6874 (mt) REVERT: h 40 TYR cc_start: 0.4778 (OUTLIER) cc_final: 0.4478 (t80) outliers start: 70 outliers final: 44 residues processed: 203 average time/residue: 0.5220 time to fit residues: 128.5675 Evaluate side-chains 191 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 277 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 313 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B1010 GLN C 239 GLN C 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105021 restraints weight = 38328.041| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.31 r_work: 0.3240 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26600 Z= 0.227 Angle : 0.701 19.391 36272 Z= 0.350 Chirality : 0.050 0.389 4212 Planarity : 0.005 0.067 4615 Dihedral : 7.181 86.351 4434 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.33 % Favored : 93.51 % Rotamer: Outliers : 2.81 % Allowed : 14.26 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3176 helix: 1.66 (0.19), residues: 791 sheet: 0.04 (0.19), residues: 696 loop : -1.80 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 905 TYR 0.023 0.002 TYR h 14 PHE 0.022 0.002 PHE B 133 TRP 0.022 0.002 TRP B 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00559 (26518) covalent geometry : angle 0.66922 (36063) SS BOND : bond 0.00738 ( 37) SS BOND : angle 2.29183 ( 74) hydrogen bonds : bond 0.06054 ( 989) hydrogen bonds : angle 5.34905 ( 2850) link_BETA1-4 : bond 0.00389 ( 7) link_BETA1-4 : angle 1.28546 ( 21) link_NAG-ASN : bond 0.00610 ( 38) link_NAG-ASN : angle 3.27978 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 138 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7266 (tm130) REVERT: A 168 PHE cc_start: 0.7127 (t80) cc_final: 0.6042 (t80) REVERT: A 309 GLU cc_start: 0.7590 (pm20) cc_final: 0.7326 (pm20) REVERT: A 361 CYS cc_start: 0.2085 (OUTLIER) cc_final: 0.1068 (p) REVERT: A 564 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7454 (mm-40) REVERT: A 574 ASP cc_start: 0.7446 (m-30) cc_final: 0.7136 (p0) REVERT: A 581 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7499 (p) REVERT: A 646 ARG cc_start: 0.8356 (tpt170) cc_final: 0.8093 (mmt180) REVERT: A 670 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7745 (pt) REVERT: B 236 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.7113 (p) REVERT: B 342 PHE cc_start: 0.7878 (m-80) cc_final: 0.7640 (m-80) REVERT: B 347 PHE cc_start: 0.5956 (m-10) cc_final: 0.5740 (m-10) REVERT: B 355 ARG cc_start: 0.7283 (ttm170) cc_final: 0.6954 (tpp-160) REVERT: B 434 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.5172 (mt) REVERT: B 440 ASN cc_start: 0.7976 (m-40) cc_final: 0.7583 (p0) REVERT: B 581 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7719 (p) REVERT: B 641 ASN cc_start: 0.7547 (t0) cc_final: 0.7172 (p0) REVERT: B 770 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7079 (mt) REVERT: C 190 ARG cc_start: 0.5780 (mmt90) cc_final: 0.5359 (mmm-85) REVERT: C 202 LYS cc_start: 0.6931 (mtpt) cc_final: 0.6551 (mptt) REVERT: C 420 ASP cc_start: 0.6678 (t0) cc_final: 0.6340 (t0) REVERT: C 495 TYR cc_start: 0.5721 (m-80) cc_final: 0.5400 (m-80) REVERT: C 528 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7344 (mmmm) REVERT: C 660 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.6661 (p90) REVERT: C 671 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8342 (p) REVERT: C 995 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7550 (mtt180) REVERT: P 3 MET cc_start: 0.4065 (tpp) cc_final: 0.3753 (tpt) REVERT: P 33 PHE cc_start: 0.6307 (m-80) cc_final: 0.6006 (m-80) REVERT: P 36 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6939 (mt) REVERT: h 40 TYR cc_start: 0.5196 (OUTLIER) cc_final: 0.4879 (t80) outliers start: 79 outliers final: 53 residues processed: 208 average time/residue: 0.5269 time to fit residues: 132.6368 Evaluate side-chains 196 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 132 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 38 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 281 optimal weight: 0.6980 chunk 261 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 171 optimal weight: 0.4980 chunk 280 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN B1010 GLN C 239 GLN C 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.176570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107725 restraints weight = 38353.163| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.32 r_work: 0.3295 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26600 Z= 0.118 Angle : 0.612 19.059 36272 Z= 0.303 Chirality : 0.046 0.385 4212 Planarity : 0.004 0.068 4615 Dihedral : 6.719 85.236 4434 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 2.17 % Allowed : 15.00 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3176 helix: 2.03 (0.19), residues: 790 sheet: 0.11 (0.19), residues: 704 loop : -1.66 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG h 35 TYR 0.023 0.001 TYR h 14 PHE 0.024 0.001 PHE h 33 TRP 0.028 0.001 TRP B 436 HIS 0.004 0.001 HIS h 15 Details of bonding type rmsd covalent geometry : bond 0.00264 (26518) covalent geometry : angle 0.58355 (36063) SS BOND : bond 0.00460 ( 37) SS BOND : angle 1.67274 ( 74) hydrogen bonds : bond 0.04486 ( 989) hydrogen bonds : angle 5.05367 ( 2850) link_BETA1-4 : bond 0.00464 ( 7) link_BETA1-4 : angle 1.06957 ( 21) link_NAG-ASN : bond 0.00607 ( 38) link_NAG-ASN : angle 3.06868 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6352 Ramachandran restraints generated. 3176 Oldfield, 0 Emsley, 3176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 145 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7151 (tm130) REVERT: A 168 PHE cc_start: 0.7187 (t80) cc_final: 0.6178 (t80) REVERT: A 309 GLU cc_start: 0.7560 (pm20) cc_final: 0.7297 (pm20) REVERT: A 361 CYS cc_start: 0.2173 (OUTLIER) cc_final: 0.0980 (p) REVERT: A 564 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7402 (mm-40) REVERT: A 574 ASP cc_start: 0.7437 (m-30) cc_final: 0.7176 (p0) REVERT: A 581 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7559 (p) REVERT: A 670 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7585 (pt) REVERT: B 236 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.7082 (p) REVERT: B 271 GLN cc_start: 0.7565 (mp10) cc_final: 0.7338 (mp10) REVERT: B 342 PHE cc_start: 0.7858 (m-80) cc_final: 0.7576 (m-80) REVERT: B 347 PHE cc_start: 0.5929 (m-10) cc_final: 0.5718 (m-10) REVERT: B 355 ARG cc_start: 0.6921 (ttm170) cc_final: 0.6647 (tpp-160) REVERT: B 440 ASN cc_start: 0.7888 (m-40) cc_final: 0.7561 (p0) REVERT: B 581 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7651 (p) REVERT: B 641 ASN cc_start: 0.7511 (t0) cc_final: 0.7040 (p0) REVERT: C 190 ARG cc_start: 0.5514 (mmt90) cc_final: 0.5096 (mmm-85) REVERT: C 202 LYS cc_start: 0.6910 (mtpt) cc_final: 0.6509 (mptt) REVERT: C 420 ASP cc_start: 0.6761 (t0) cc_final: 0.6429 (t0) REVERT: C 495 TYR cc_start: 0.5814 (m-80) cc_final: 0.5232 (m-80) REVERT: C 528 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7243 (mttm) REVERT: C 660 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6003 (p90) REVERT: C 671 CYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8282 (p) REVERT: C 740 MET cc_start: 0.8246 (ttt) cc_final: 0.7704 (ttm) REVERT: C 995 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7490 (mtt180) REVERT: P 3 MET cc_start: 0.4076 (tpp) cc_final: 0.3759 (tpt) REVERT: P 33 PHE cc_start: 0.6231 (m-80) cc_final: 0.5978 (m-80) REVERT: P 36 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6848 (mt) REVERT: h 40 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.4660 (t80) outliers start: 61 outliers final: 44 residues processed: 196 average time/residue: 0.4807 time to fit residues: 115.4240 Evaluate side-chains 188 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 92 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN B1010 GLN C 360 ASN C 703 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.174622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105813 restraints weight = 38176.771| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.34 r_work: 0.3247 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26600 Z= 0.205 Angle : 0.681 19.228 36272 Z= 0.339 Chirality : 0.049 0.391 4212 Planarity : 0.005 0.067 4615 Dihedral : 6.942 84.598 4434 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 2.35 % Allowed : 14.93 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3176 helix: 1.79 (0.19), residues: 791 sheet: 0.05 (0.20), residues: 697 loop : -1.72 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG h 35 TYR 0.027 0.002 TYR h 14 PHE 0.027 0.002 PHE h 33 TRP 0.026 0.002 TRP B 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00506 (26518) covalent geometry : angle 0.65097 (36063) SS BOND : bond 0.00736 ( 37) SS BOND : angle 2.12573 ( 74) hydrogen bonds : bond 0.05673 ( 989) hydrogen bonds : angle 5.24407 ( 2850) link_BETA1-4 : bond 0.00404 ( 7) link_BETA1-4 : angle 1.20497 ( 21) link_NAG-ASN : bond 0.00598 ( 38) link_NAG-ASN : angle 3.21085 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13946.02 seconds wall clock time: 236 minutes 52.20 seconds (14212.20 seconds total)