Starting phenix.real_space_refine on Sun Jun 22 17:06:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zss_14947/06_2025/7zss_14947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zss_14947/06_2025/7zss_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_14947/06_2025/7zss_14947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zss_14947/06_2025/7zss_14947.map" model { file = "/net/cci-nas-00/data/ceres_data/7zss_14947/06_2025/7zss_14947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zss_14947/06_2025/7zss_14947.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.49, per 1000 atoms: 0.64 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: 7.12 Conformation dependent library (CDL) restraints added in 3.6 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: 3.84 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: 10.86 Time building geometry restraints manager: 8.32 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 1146 or resid 1201 through 1208)) selection = (chain 'B' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 1201 through 1208)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 1201 through 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 62.790 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (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 TRP 0.016 0.001 TRP A 886 HIS 0.010 0.001 HIS P 15 PHE 0.028 0.001 PHE D 33 TYR 0.024 0.001 TYR h 14 ARG 0.008 0.000 ARG h 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 38) link_NAG-ASN : angle 3.09392 ( 114) link_BETA1-4 : bond 0.00568 ( 7) link_BETA1-4 : angle 1.07664 ( 21) hydrogen bonds : bond 0.19305 ( 989) hydrogen bonds : angle 7.74564 ( 2850) SS BOND : bond 0.00400 ( 37) SS BOND : angle 1.32858 ( 74) covalent geometry : bond 0.00426 (26518) covalent geometry : angle 0.69819 (36063) *********************** 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 : 3.051 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: 0.5207 (tptm) REVERT: A 168 PHE cc_start: 0.7017 (t80) cc_final: 0.6479 (t80) REVERT: A 190 ARG cc_start: 0.6612 (mtt90) cc_final: 0.6007 (mmt-90) 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: 0.7644 (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 33 PHE cc_start: 0.6262 (m-10) cc_final: 0.6060 (m-80) REVERT: P 36 ILE cc_start: 0.6651 (mp) cc_final: 0.6322 (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: 0.3902 (t80) outliers start: 0 outliers final: 1 residues processed: 302 average time/residue: 1.0854 time to fit residues: 395.3708 Evaluate side-chains 160 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 2.929 ------------------------------------------------------------------------------- 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 271 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 83 optimal weight: 0.2980 chunk 164 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 218 GLN B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 196 ASN C 207 HIS C 703 ASN C1106 GLN P 12 GLN P 15 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.177408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106776 restraints weight = 38101.569| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.36 r_work: 0.3280 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26600 Z= 0.205 Angle : 0.718 19.307 36272 Z= 0.359 Chirality : 0.051 0.391 4212 Planarity : 0.005 0.098 4615 Dihedral : 10.052 105.428 4434 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.82 % Favored : 93.99 % Rotamer: Outliers : 1.32 % Allowed : 7.75 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3176 helix: 1.83 (0.19), residues: 792 sheet: 0.10 (0.20), residues: 708 loop : -1.79 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.008 0.001 HIS P 15 PHE 0.028 0.002 PHE C 377 TYR 0.029 0.002 TYR B1067 ARG 0.006 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 38) link_NAG-ASN : angle 3.17190 ( 114) link_BETA1-4 : bond 0.00557 ( 7) link_BETA1-4 : angle 1.26823 ( 21) hydrogen bonds : bond 0.05823 ( 989) hydrogen bonds : angle 5.75309 ( 2850) SS BOND : bond 0.00703 ( 37) SS BOND : angle 2.06093 ( 74) covalent geometry : bond 0.00504 (26518) covalent geometry : angle 0.69080 (36063) *********************** 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 212 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7125 (tm130) REVERT: A 129 LYS cc_start: 0.5223 (mttp) cc_final: 0.4664 (tptm) REVERT: A 168 PHE cc_start: 0.7116 (t80) cc_final: 0.6244 (t80) REVERT: A 207 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6978 (t70) REVERT: A 869 MET cc_start: 0.9052 (mtt) cc_final: 0.8852 (mtt) REVERT: B 111 ASP cc_start: 0.4859 (t0) cc_final: 0.4418 (p0) REVERT: B 188 ASN cc_start: 0.6887 (m-40) cc_final: 0.6372 (p0) REVERT: B 191 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: B 202 LYS cc_start: 0.7565 (mttp) cc_final: 0.6940 (mtmm) REVERT: B 342 PHE cc_start: 0.7868 (m-80) cc_final: 0.7542 (m-80) REVERT: B 347 PHE cc_start: 0.4675 (m-10) cc_final: 0.4213 (m-10) REVERT: B 392 PHE cc_start: 0.6166 (m-80) cc_final: 0.5959 (m-80) REVERT: B 440 ASN cc_start: 0.7978 (m-40) cc_final: 0.7621 (p0) REVERT: B 564 GLN cc_start: 0.5802 (tm-30) cc_final: 0.5093 (tm-30) REVERT: B 574 ASP cc_start: 0.7031 (t70) cc_final: 0.6824 (t0) REVERT: C 201 PHE cc_start: 0.4837 (m-80) cc_final: 0.4072 (t80) REVERT: C 202 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6371 (mptt) REVERT: C 380 TYR cc_start: 0.7826 (m-80) cc_final: 0.7551 (m-10) REVERT: C 420 ASP cc_start: 0.6736 (m-30) cc_final: 0.6420 (t0) REVERT: C 495 TYR cc_start: 0.6066 (m-80) cc_final: 0.5604 (m-80) REVERT: C 515 PHE cc_start: 0.6758 (m-10) cc_final: 0.6518 (m-80) REVERT: C 703 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8081 (p0) REVERT: C 868 GLU cc_start: 0.8180 (mp0) cc_final: 0.7851 (mt-10) REVERT: P 3 MET cc_start: 0.3732 (tpp) cc_final: 0.3044 (tmt) REVERT: P 33 PHE cc_start: 0.6200 (m-10) cc_final: 0.5817 (m-80) REVERT: h 17 GLN cc_start: 0.5166 (pt0) cc_final: 0.4898 (pt0) REVERT: h 39 GLN cc_start: 0.8386 (tp40) cc_final: 0.7887 (tm-30) REVERT: h 40 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.5236 (t80) REVERT: h 44 ILE cc_start: 0.4148 (OUTLIER) cc_final: 0.3852 (pp) REVERT: h 47 TYR cc_start: 0.4226 (t80) cc_final: 0.3657 (t80) outliers start: 37 outliers final: 12 residues processed: 202 average time/residue: 1.0814 time to fit residues: 266.2074 Evaluate side-chains 160 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 539 VAL 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 720 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 960 ASN 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 114 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 318 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 440 ASN A 544 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 196 ASN C 913 GLN C 914 ASN C1011 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.176472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106224 restraints weight = 37922.973| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.41 r_work: 0.3256 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26600 Z= 0.201 Angle : 0.682 19.534 36272 Z= 0.342 Chirality : 0.049 0.406 4212 Planarity : 0.005 0.081 4615 Dihedral : 8.262 96.042 4434 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.82 % Favored : 93.99 % Rotamer: Outliers : 1.78 % Allowed : 10.84 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3176 helix: 1.74 (0.19), residues: 789 sheet: 0.09 (0.20), residues: 702 loop : -1.85 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.016 0.001 HIS A 207 PHE 0.018 0.002 PHE B 133 TYR 0.022 0.002 TYR B1067 ARG 0.007 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 38) link_NAG-ASN : angle 3.22441 ( 114) link_BETA1-4 : bond 0.00377 ( 7) link_BETA1-4 : angle 1.29863 ( 21) hydrogen bonds : bond 0.05904 ( 989) hydrogen bonds : angle 5.55846 ( 2850) SS BOND : bond 0.00698 ( 37) SS BOND : angle 1.93783 ( 74) covalent geometry : bond 0.00493 (26518) covalent geometry : angle 0.65328 (36063) *********************** 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 211 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 2.792 Fit side-chains REVERT: A 52 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7149 (tm130) REVERT: A 168 PHE cc_start: 0.7090 (t80) cc_final: 0.6026 (t80) REVERT: A 207 HIS cc_start: 0.7522 (m-70) cc_final: 0.7016 (t-90) REVERT: A 309 GLU cc_start: 0.7555 (pm20) cc_final: 0.7315 (pm20) REVERT: A 396 TYR cc_start: 0.5130 (m-10) cc_final: 0.4880 (m-80) REVERT: A 869 MET cc_start: 0.9049 (mtt) cc_final: 0.8832 (mtt) REVERT: B 111 ASP cc_start: 0.5002 (t0) cc_final: 0.4546 (p0) REVERT: B 191 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 202 LYS cc_start: 0.7609 (mttp) cc_final: 0.7241 (mtpp) REVERT: B 281 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8023 (tt0) REVERT: B 342 PHE cc_start: 0.7934 (m-80) cc_final: 0.7660 (m-80) REVERT: B 347 PHE cc_start: 0.4894 (m-10) cc_final: 0.4481 (m-10) REVERT: B 440 ASN cc_start: 0.8011 (m-40) cc_final: 0.7659 (p0) REVERT: B 564 GLN cc_start: 0.5771 (tm-30) cc_final: 0.4901 (tm-30) REVERT: C 196 ASN cc_start: 0.5341 (OUTLIER) cc_final: 0.5134 (t0) REVERT: C 201 PHE cc_start: 0.4721 (m-80) cc_final: 0.3983 (t80) REVERT: C 202 LYS cc_start: 0.6760 (mtpt) cc_final: 0.6304 (mptt) REVERT: C 420 ASP cc_start: 0.6748 (m-30) cc_final: 0.6452 (t0) REVERT: C 495 TYR cc_start: 0.6017 (m-80) cc_final: 0.5600 (m-80) REVERT: C 515 PHE cc_start: 0.7072 (m-10) cc_final: 0.6842 (m-80) REVERT: C 528 LYS cc_start: 0.7604 (mmmt) cc_final: 0.7104 (mmmm) REVERT: C 540 ASN cc_start: 0.6439 (OUTLIER) cc_final: 0.6215 (p0) REVERT: C 995 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7389 (mtt180) REVERT: P 3 MET cc_start: 0.3945 (tpp) cc_final: 0.3190 (tmt) REVERT: P 33 PHE cc_start: 0.6205 (m-10) cc_final: 0.5812 (m-80) REVERT: h 17 GLN cc_start: 0.5130 (pt0) cc_final: 0.4899 (pt0) REVERT: h 39 GLN cc_start: 0.8470 (tp40) cc_final: 0.7896 (tm-30) REVERT: h 40 TYR cc_start: 0.5705 (OUTLIER) cc_final: 0.5204 (t80) REVERT: h 44 ILE cc_start: 0.4120 (OUTLIER) cc_final: 0.3808 (pp) outliers start: 50 outliers final: 28 residues processed: 200 average time/residue: 1.0762 time to fit residues: 261.1055 Evaluate side-chains 175 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 2.816 ------------------------------------------------------------------------------- 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 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 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 720 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU 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 196 ASN 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 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 1104 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 95 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 207 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1088 HIS C 196 ASN C 703 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107105 restraints weight = 38382.042| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.35 r_work: 0.3284 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2029 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= 0.144 Angle : 0.625 19.361 36272 Z= 0.312 Chirality : 0.047 0.376 4212 Planarity : 0.004 0.077 4615 Dihedral : 7.663 93.039 4434 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.64 % Favored : 94.18 % Rotamer: Outliers : 2.24 % Allowed : 11.91 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3176 helix: 1.89 (0.19), residues: 790 sheet: 0.13 (0.19), residues: 698 loop : -1.79 (0.13), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.004 0.001 HIS A 207 PHE 0.022 0.001 PHE B 133 TYR 0.021 0.001 TYR C 170 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 38) link_NAG-ASN : angle 3.14671 ( 114) link_BETA1-4 : bond 0.00462 ( 7) link_BETA1-4 : angle 1.18479 ( 21) hydrogen bonds : bond 0.05069 ( 989) hydrogen bonds : angle 5.33578 ( 2850) SS BOND : bond 0.00580 ( 37) SS BOND : angle 1.73042 ( 74) covalent geometry : bond 0.00341 (26518) covalent geometry : angle 0.59501 (36063) *********************** 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 218 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 2.808 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7169 (tm130) REVERT: A 168 PHE cc_start: 0.7023 (t80) cc_final: 0.5983 (t80) REVERT: A 207 HIS cc_start: 0.7133 (m90) cc_final: 0.6732 (t-90) REVERT: A 309 GLU cc_start: 0.7523 (pm20) cc_final: 0.7273 (pm20) REVERT: A 361 CYS cc_start: 0.2314 (OUTLIER) cc_final: 0.1465 (p) REVERT: A 396 TYR cc_start: 0.4842 (m-10) cc_final: 0.4607 (m-80) REVERT: A 403 ARG cc_start: 0.4562 (mtm-85) cc_final: 0.4306 (ttp-110) REVERT: A 869 MET cc_start: 0.9042 (mtt) cc_final: 0.8790 (mtt) REVERT: A 964 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7984 (mmpt) REVERT: A 1132 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8404 (tp) REVERT: B 111 ASP cc_start: 0.4983 (t0) cc_final: 0.4531 (p0) REVERT: B 342 PHE cc_start: 0.7908 (m-80) cc_final: 0.7647 (m-80) REVERT: B 347 PHE cc_start: 0.4882 (m-10) cc_final: 0.4460 (m-10) REVERT: B 355 ARG cc_start: 0.6963 (ttm170) cc_final: 0.6558 (tpp-160) REVERT: B 440 ASN cc_start: 0.7995 (m-40) cc_final: 0.7641 (p0) REVERT: B 564 GLN cc_start: 0.5825 (tm-30) cc_final: 0.4868 (tm-30) REVERT: C 194 PHE cc_start: 0.6639 (m-10) cc_final: 0.6434 (m-80) REVERT: C 201 PHE cc_start: 0.4810 (m-80) cc_final: 0.4150 (t80) REVERT: C 202 LYS cc_start: 0.6722 (mtpt) cc_final: 0.6168 (mptt) REVERT: C 420 ASP cc_start: 0.6715 (m-30) cc_final: 0.6418 (t0) REVERT: C 495 TYR cc_start: 0.6007 (m-80) cc_final: 0.5574 (m-80) REVERT: C 528 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7138 (mmmm) REVERT: C 540 ASN cc_start: 0.6505 (OUTLIER) cc_final: 0.6274 (p0) REVERT: C 660 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6376 (p90) REVERT: C 671 CYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 703 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7970 (p0) REVERT: C 995 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7417 (mtt180) REVERT: P 33 PHE cc_start: 0.6237 (m-10) cc_final: 0.5858 (m-80) REVERT: h 39 GLN cc_start: 0.8466 (tp40) cc_final: 0.7855 (tm-30) REVERT: h 40 TYR cc_start: 0.5621 (OUTLIER) cc_final: 0.5174 (t80) REVERT: h 44 ILE cc_start: 0.4050 (OUTLIER) cc_final: 0.3729 (pp) outliers start: 63 outliers final: 32 residues processed: 208 average time/residue: 0.9804 time to fit residues: 250.1896 Evaluate side-chains 180 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 539 VAL 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 964 LYS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 551 VAL 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 B residue 1120 THR 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 560 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL 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 1122 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 440 ASN B 774 GLN C 703 ASN h 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.177201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108037 restraints weight = 38256.584| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.33 r_work: 0.3285 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2155 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= 0.141 Angle : 0.619 19.377 36272 Z= 0.308 Chirality : 0.047 0.381 4212 Planarity : 0.004 0.071 4615 Dihedral : 7.397 91.691 4434 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 2.56 % Allowed : 12.83 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3176 helix: 1.90 (0.19), residues: 797 sheet: 0.11 (0.19), residues: 700 loop : -1.75 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.003 0.001 HIS D 15 PHE 0.026 0.001 PHE B 168 TYR 0.021 0.001 TYR B 351 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 38) link_NAG-ASN : angle 3.12587 ( 114) link_BETA1-4 : bond 0.00405 ( 7) link_BETA1-4 : angle 1.14214 ( 21) hydrogen bonds : bond 0.04933 ( 989) hydrogen bonds : angle 5.24685 ( 2850) SS BOND : bond 0.00561 ( 37) SS BOND : angle 1.72239 ( 74) covalent geometry : bond 0.00334 (26518) covalent geometry : angle 0.58941 (36063) *********************** 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 220 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 148 time to evaluate : 2.704 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7558 (tm-30) cc_final: 0.7169 (tm130) REVERT: A 168 PHE cc_start: 0.7090 (t80) cc_final: 0.5955 (t80) REVERT: A 207 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6780 (t-90) REVERT: A 309 GLU cc_start: 0.7507 (pm20) cc_final: 0.7242 (pm20) REVERT: A 361 CYS cc_start: 0.1916 (OUTLIER) cc_final: 0.1435 (p) REVERT: A 396 TYR cc_start: 0.4878 (m-10) cc_final: 0.4634 (m-80) REVERT: A 670 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7551 (pt) REVERT: A 869 MET cc_start: 0.9015 (mtt) cc_final: 0.8743 (mtt) REVERT: A 964 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7986 (mmpt) REVERT: A 1132 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8343 (tp) REVERT: B 111 ASP cc_start: 0.4962 (t0) cc_final: 0.4520 (p0) REVERT: B 342 PHE cc_start: 0.7915 (m-80) cc_final: 0.7675 (m-80) REVERT: B 347 PHE cc_start: 0.4973 (m-10) cc_final: 0.4505 (m-10) REVERT: B 355 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6695 (tpp-160) REVERT: B 434 ILE cc_start: 0.5267 (OUTLIER) cc_final: 0.4720 (mm) REVERT: B 440 ASN cc_start: 0.7995 (m-40) cc_final: 0.7639 (p0) REVERT: B 564 GLN cc_start: 0.5935 (tm-30) cc_final: 0.4908 (tm-30) REVERT: B 581 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7849 (p) REVERT: C 201 PHE cc_start: 0.4763 (m-80) cc_final: 0.4067 (t80) REVERT: C 202 LYS cc_start: 0.6805 (mtpt) cc_final: 0.6234 (mptt) REVERT: C 420 ASP cc_start: 0.6718 (m-30) cc_final: 0.6507 (t0) REVERT: C 495 TYR cc_start: 0.5655 (m-80) cc_final: 0.5242 (m-80) REVERT: C 528 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7115 (mmmm) REVERT: C 540 ASN cc_start: 0.6484 (OUTLIER) cc_final: 0.6250 (p0) REVERT: C 660 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6320 (p90) REVERT: C 671 CYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8271 (p) REVERT: C 703 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8022 (p0) REVERT: C 995 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7406 (mtt180) REVERT: P 3 MET cc_start: 0.3328 (tmm) cc_final: 0.3091 (tpt) REVERT: P 33 PHE cc_start: 0.6281 (m-10) cc_final: 0.6074 (m-80) REVERT: P 36 ILE cc_start: 0.7007 (mp) cc_final: 0.6714 (mt) REVERT: h 40 TYR cc_start: 0.5648 (OUTLIER) cc_final: 0.5326 (t80) REVERT: h 44 ILE cc_start: 0.4072 (OUTLIER) cc_final: 0.3771 (pp) outliers start: 72 outliers final: 43 residues processed: 209 average time/residue: 0.9512 time to fit residues: 247.6484 Evaluate side-chains 194 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 2.866 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain A residue 964 LYS 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 197 ILE 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 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 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 740 MET 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 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 540 ASN 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 703 ASN 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 859 THR Chi-restraints excluded: chain C residue 878 LEU 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 53 VAL 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 227 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 320 optimal weight: 0.0270 chunk 127 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 232 optimal weight: 0.0770 chunk 307 optimal weight: 20.0000 chunk 72 optimal weight: 0.0070 overall best weight: 1.0218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN C 703 ASN h 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107874 restraints weight = 38173.578| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.34 r_work: 0.3296 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26600 Z= 0.125 Angle : 0.604 19.284 36272 Z= 0.300 Chirality : 0.046 0.442 4212 Planarity : 0.004 0.070 4615 Dihedral : 7.108 90.439 4434 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 2.56 % Allowed : 13.22 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3176 helix: 2.05 (0.19), residues: 790 sheet: 0.17 (0.19), residues: 694 loop : -1.66 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 436 HIS 0.003 0.001 HIS P 15 PHE 0.021 0.001 PHE B 133 TYR 0.021 0.001 TYR C 170 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 38) link_NAG-ASN : angle 3.07324 ( 114) link_BETA1-4 : bond 0.00426 ( 7) link_BETA1-4 : angle 1.10305 ( 21) hydrogen bonds : bond 0.04623 ( 989) hydrogen bonds : angle 5.14526 ( 2850) SS BOND : bond 0.00498 ( 37) SS BOND : angle 1.63744 ( 74) covalent geometry : bond 0.00290 (26518) covalent geometry : angle 0.57472 (36063) *********************** 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 221 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 149 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7068 (tm130) REVERT: A 168 PHE cc_start: 0.7115 (t80) cc_final: 0.5993 (t80) REVERT: A 207 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6793 (t-90) REVERT: A 309 GLU cc_start: 0.7506 (pm20) cc_final: 0.7236 (pm20) REVERT: A 361 CYS cc_start: 0.1917 (OUTLIER) cc_final: 0.1413 (p) REVERT: A 396 TYR cc_start: 0.4840 (m-10) cc_final: 0.4605 (m-80) REVERT: A 670 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7536 (pt) REVERT: A 869 MET cc_start: 0.9013 (mtt) cc_final: 0.8742 (mtt) REVERT: A 964 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7987 (mmpt) REVERT: A 1132 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8293 (tp) REVERT: B 111 ASP cc_start: 0.4893 (t0) cc_final: 0.4398 (p0) REVERT: B 342 PHE cc_start: 0.7901 (m-80) cc_final: 0.7678 (m-80) REVERT: B 347 PHE cc_start: 0.5334 (m-10) cc_final: 0.5032 (m-10) REVERT: B 355 ARG cc_start: 0.7126 (ttm170) cc_final: 0.6696 (tpp-160) REVERT: B 434 ILE cc_start: 0.5240 (OUTLIER) cc_final: 0.4684 (mm) REVERT: B 440 ASN cc_start: 0.7987 (m-40) cc_final: 0.7629 (p0) REVERT: B 564 GLN cc_start: 0.5944 (tm-30) cc_final: 0.4878 (tm-30) REVERT: B 581 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7843 (p) REVERT: C 201 PHE cc_start: 0.4689 (m-80) cc_final: 0.4032 (t80) REVERT: C 202 LYS cc_start: 0.6844 (mtpt) cc_final: 0.6285 (mptt) REVERT: C 239 GLN cc_start: 0.6723 (mp10) cc_final: 0.6432 (mt0) REVERT: C 420 ASP cc_start: 0.6700 (m-30) cc_final: 0.6492 (t0) REVERT: C 495 TYR cc_start: 0.5751 (m-80) cc_final: 0.5219 (m-80) REVERT: C 528 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7203 (mmmm) REVERT: C 540 ASN cc_start: 0.6494 (OUTLIER) cc_final: 0.6257 (p0) REVERT: C 658 ASN cc_start: 0.7391 (t0) cc_final: 0.6917 (m110) REVERT: C 660 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.6204 (p90) REVERT: C 671 CYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8279 (p) REVERT: C 703 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.8002 (p0) REVERT: C 995 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7383 (mtt180) REVERT: P 3 MET cc_start: 0.3411 (tmm) cc_final: 0.3187 (tpt) REVERT: P 36 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6690 (mt) REVERT: h 40 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.5285 (t80) REVERT: h 44 ILE cc_start: 0.4079 (OUTLIER) cc_final: 0.3741 (pp) outliers start: 72 outliers final: 42 residues processed: 206 average time/residue: 0.9528 time to fit residues: 243.9001 Evaluate side-chains 196 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 2.681 ------------------------------------------------------------------------------- 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 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 964 LYS 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 127 VAL Chi-restraints excluded: chain B residue 197 ILE 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 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 740 MET Chi-restraints excluded: chain B residue 754 LEU 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 540 ASN 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 703 ASN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 296 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 246 optimal weight: 0.4980 chunk 273 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 304 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN C 703 ASN P 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.177674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109003 restraints weight = 38445.195| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.33 r_work: 0.3297 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26600 Z= 0.127 Angle : 0.602 19.254 36272 Z= 0.298 Chirality : 0.046 0.389 4212 Planarity : 0.004 0.068 4615 Dihedral : 6.904 89.258 4434 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.33 % Rotamer: Outliers : 2.84 % Allowed : 13.51 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3176 helix: 2.06 (0.19), residues: 791 sheet: 0.18 (0.19), residues: 695 loop : -1.64 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS P 15 PHE 0.028 0.001 PHE B 168 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 38) link_NAG-ASN : angle 3.05265 ( 114) link_BETA1-4 : bond 0.00443 ( 7) link_BETA1-4 : angle 1.08635 ( 21) hydrogen bonds : bond 0.04576 ( 989) hydrogen bonds : angle 5.10045 ( 2850) SS BOND : bond 0.00499 ( 37) SS BOND : angle 1.60806 ( 74) covalent geometry : bond 0.00295 (26518) covalent geometry : angle 0.57343 (36063) *********************** 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 227 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 147 time to evaluate : 2.724 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7066 (tm130) REVERT: A 168 PHE cc_start: 0.7103 (t80) cc_final: 0.5891 (t80) REVERT: A 207 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6927 (t-90) REVERT: A 309 GLU cc_start: 0.7518 (pm20) cc_final: 0.7240 (pm20) REVERT: A 361 CYS cc_start: 0.1844 (OUTLIER) cc_final: 0.1361 (p) REVERT: A 670 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7533 (pt) REVERT: A 869 MET cc_start: 0.9020 (mtt) cc_final: 0.8744 (mtt) REVERT: A 964 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7995 (mmpt) REVERT: A 1132 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8265 (tp) REVERT: B 111 ASP cc_start: 0.4886 (t0) cc_final: 0.4440 (p0) REVERT: B 188 ASN cc_start: 0.6890 (m-40) cc_final: 0.6561 (p0) REVERT: B 342 PHE cc_start: 0.7896 (m-80) cc_final: 0.7668 (m-80) REVERT: B 347 PHE cc_start: 0.5621 (m-10) cc_final: 0.5275 (m-10) REVERT: B 355 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6751 (tpp-160) REVERT: B 434 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.4678 (mm) REVERT: B 440 ASN cc_start: 0.7873 (m-40) cc_final: 0.7579 (p0) REVERT: B 581 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 740 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8193 (mmm) REVERT: C 201 PHE cc_start: 0.4726 (m-80) cc_final: 0.4077 (t80) REVERT: C 202 LYS cc_start: 0.6819 (mtpt) cc_final: 0.6292 (mptt) REVERT: C 239 GLN cc_start: 0.6625 (mp10) cc_final: 0.6381 (mt0) REVERT: C 420 ASP cc_start: 0.6698 (m-30) cc_final: 0.6487 (t0) REVERT: C 495 TYR cc_start: 0.5765 (m-80) cc_final: 0.5125 (m-80) REVERT: C 528 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7215 (mmmm) REVERT: C 660 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.6268 (p90) REVERT: C 671 CYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8242 (p) REVERT: C 995 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7380 (mtt180) REVERT: P 3 MET cc_start: 0.3428 (tmm) cc_final: 0.3199 (tpt) REVERT: P 33 PHE cc_start: 0.6131 (m-80) cc_final: 0.5899 (m-80) REVERT: P 36 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6676 (mt) REVERT: h 40 TYR cc_start: 0.5701 (OUTLIER) cc_final: 0.5363 (t80) REVERT: h 44 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3697 (pp) outliers start: 80 outliers final: 46 residues processed: 212 average time/residue: 0.9998 time to fit residues: 264.8427 Evaluate side-chains 201 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 142 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL 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 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 964 LYS 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 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 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 740 MET 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 325 SER Chi-restraints excluded: chain C residue 450 ASN 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 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 Chi-restraints excluded: chain h residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 126 optimal weight: 0.0980 chunk 229 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 440 ASN A 544 ASN P 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109259 restraints weight = 38440.986| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.35 r_work: 0.3319 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26600 Z= 0.111 Angle : 0.581 19.113 36272 Z= 0.287 Chirality : 0.045 0.394 4212 Planarity : 0.004 0.068 4615 Dihedral : 6.580 87.271 4434 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 2.60 % Allowed : 13.76 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3176 helix: 2.19 (0.19), residues: 791 sheet: 0.21 (0.19), residues: 697 loop : -1.57 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 436 HIS 0.005 0.000 HIS h 15 PHE 0.021 0.001 PHE h 33 TYR 0.025 0.001 TYR B 351 ARG 0.006 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 38) link_NAG-ASN : angle 2.98870 ( 114) link_BETA1-4 : bond 0.00456 ( 7) link_BETA1-4 : angle 1.03279 ( 21) hydrogen bonds : bond 0.04126 ( 989) hydrogen bonds : angle 4.93962 ( 2850) SS BOND : bond 0.00451 ( 37) SS BOND : angle 1.43895 ( 74) covalent geometry : bond 0.00251 (26518) covalent geometry : angle 0.55307 (36063) *********************** 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 215 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 142 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7062 (tm130) REVERT: A 168 PHE cc_start: 0.6989 (t80) cc_final: 0.5985 (t80) REVERT: A 207 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6987 (t-90) REVERT: A 309 GLU cc_start: 0.7531 (pm20) cc_final: 0.7258 (pm20) REVERT: A 361 CYS cc_start: 0.1859 (OUTLIER) cc_final: 0.1329 (p) REVERT: A 581 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7591 (p) REVERT: A 670 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7476 (pt) REVERT: A 869 MET cc_start: 0.9025 (mtt) cc_final: 0.8760 (mtt) REVERT: A 964 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7887 (mmpt) REVERT: A 1132 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8154 (tp) REVERT: B 188 ASN cc_start: 0.6866 (m-40) cc_final: 0.6559 (p0) REVERT: B 342 PHE cc_start: 0.7875 (m-80) cc_final: 0.7653 (m-80) REVERT: B 347 PHE cc_start: 0.5645 (m-10) cc_final: 0.5292 (m-10) REVERT: B 355 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6766 (tpp-160) REVERT: B 434 ILE cc_start: 0.5196 (OUTLIER) cc_final: 0.4686 (mm) REVERT: B 440 ASN cc_start: 0.7837 (m-40) cc_final: 0.7507 (p0) REVERT: B 581 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 740 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8162 (mmm) REVERT: C 201 PHE cc_start: 0.4695 (m-80) cc_final: 0.4128 (t80) REVERT: C 202 LYS cc_start: 0.6807 (mtpt) cc_final: 0.6288 (mptt) REVERT: C 420 ASP cc_start: 0.6657 (m-30) cc_final: 0.6353 (t0) REVERT: C 495 TYR cc_start: 0.5780 (m-80) cc_final: 0.5035 (m-80) REVERT: C 528 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7214 (mmmm) REVERT: C 660 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.6186 (p90) REVERT: C 671 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8232 (p) REVERT: C 995 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7363 (mtt180) REVERT: P 3 MET cc_start: 0.3433 (tmm) cc_final: 0.3181 (tpt) REVERT: P 36 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6679 (mt) REVERT: h 40 TYR cc_start: 0.5592 (OUTLIER) cc_final: 0.5346 (t80) REVERT: h 44 ILE cc_start: 0.4088 (OUTLIER) cc_final: 0.3759 (pp) outliers start: 73 outliers final: 39 residues processed: 205 average time/residue: 0.9525 time to fit residues: 242.5031 Evaluate side-chains 182 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL 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 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 878 LEU Chi-restraints excluded: chain A residue 964 LYS 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 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 224 GLU 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 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 740 MET 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 307 THR Chi-restraints excluded: chain C residue 325 SER 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 1104 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 Chi-restraints excluded: chain h residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 301 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 219 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- 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 A 440 ASN A 544 ASN C 239 GLN P 15 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.175783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106266 restraints weight = 38437.900| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.33 r_work: 0.3274 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26600 Z= 0.167 Angle : 0.640 19.263 36272 Z= 0.318 Chirality : 0.048 0.394 4212 Planarity : 0.004 0.067 4615 Dihedral : 6.759 86.083 4434 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.98 % Favored : 93.86 % Rotamer: Outliers : 2.35 % Allowed : 14.18 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3176 helix: 1.94 (0.19), residues: 792 sheet: 0.20 (0.19), residues: 707 loop : -1.67 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 PHE 0.023 0.002 PHE B 168 TYR 0.020 0.002 TYR B1067 ARG 0.006 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 38) link_NAG-ASN : angle 3.11109 ( 114) link_BETA1-4 : bond 0.00425 ( 7) link_BETA1-4 : angle 1.14664 ( 21) hydrogen bonds : bond 0.05192 ( 989) hydrogen bonds : angle 5.12122 ( 2850) SS BOND : bond 0.00617 ( 37) SS BOND : angle 1.92742 ( 74) covalent geometry : bond 0.00405 (26518) covalent geometry : angle 0.61102 (36063) *********************** 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 206 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7085 (tm130) REVERT: A 168 PHE cc_start: 0.7007 (t80) cc_final: 0.5923 (t80) REVERT: A 207 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.7114 (t-90) REVERT: A 309 GLU cc_start: 0.7561 (pm20) cc_final: 0.7283 (pm20) REVERT: A 564 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7434 (mm-40) REVERT: A 581 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7577 (p) REVERT: A 670 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7570 (pt) REVERT: A 869 MET cc_start: 0.9029 (mtt) cc_final: 0.8824 (mtt) REVERT: A 1132 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8357 (tp) REVERT: B 188 ASN cc_start: 0.6887 (m-40) cc_final: 0.6585 (p0) REVERT: B 342 PHE cc_start: 0.7879 (m-80) cc_final: 0.7622 (m-80) REVERT: B 347 PHE cc_start: 0.5786 (m-10) cc_final: 0.5509 (m-10) REVERT: B 355 ARG cc_start: 0.7224 (ttm170) cc_final: 0.6681 (tpp-160) REVERT: B 434 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.5002 (mt) REVERT: B 440 ASN cc_start: 0.7855 (m-40) cc_final: 0.7521 (p0) REVERT: B 581 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 740 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8309 (mmm) REVERT: B 770 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7123 (mt) REVERT: C 201 PHE cc_start: 0.4739 (m-80) cc_final: 0.4076 (t80) REVERT: C 202 LYS cc_start: 0.6839 (mtpt) cc_final: 0.6427 (mptt) REVERT: C 291 CYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6893 (m) REVERT: C 420 ASP cc_start: 0.6603 (m-30) cc_final: 0.6359 (t0) REVERT: C 495 TYR cc_start: 0.5868 (m-80) cc_final: 0.5140 (m-80) REVERT: C 528 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7300 (mmmm) REVERT: C 660 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.6369 (p90) REVERT: C 671 CYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8222 (p) REVERT: C 995 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7453 (mtt180) REVERT: P 3 MET cc_start: 0.3441 (tmm) cc_final: 0.3188 (tpt) REVERT: P 36 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6653 (mt) REVERT: h 40 TYR cc_start: 0.5575 (OUTLIER) cc_final: 0.5340 (t80) outliers start: 66 outliers final: 45 residues processed: 197 average time/residue: 1.0056 time to fit residues: 252.1142 Evaluate side-chains 187 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL 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 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 1132 ILE 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 197 ILE Chi-restraints excluded: chain B residue 224 GLU 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 514 SER Chi-restraints excluded: chain B residue 515 PHE 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 740 MET Chi-restraints excluded: chain B residue 770 ILE 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 291 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 450 ASN 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 285 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 319 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 313 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 B 914 ASN C 239 GLN P 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108073 restraints weight = 38332.895| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.33 r_work: 0.3299 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26600 Z= 0.122 Angle : 0.594 19.065 36272 Z= 0.295 Chirality : 0.046 0.390 4212 Planarity : 0.004 0.068 4615 Dihedral : 6.545 84.717 4434 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 2.13 % Allowed : 14.68 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3176 helix: 2.13 (0.19), residues: 785 sheet: 0.21 (0.19), residues: 700 loop : -1.60 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 436 HIS 0.003 0.001 HIS h 15 PHE 0.030 0.001 PHE h 33 TYR 0.026 0.001 TYR B 351 ARG 0.004 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 38) link_NAG-ASN : angle 3.02609 ( 114) link_BETA1-4 : bond 0.00435 ( 7) link_BETA1-4 : angle 1.04948 ( 21) hydrogen bonds : bond 0.04458 ( 989) hydrogen bonds : angle 5.00011 ( 2850) SS BOND : bond 0.00501 ( 37) SS BOND : angle 1.60806 ( 74) covalent geometry : bond 0.00282 (26518) covalent geometry : angle 0.56565 (36063) ********************** 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 194 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7046 (tm130) REVERT: A 168 PHE cc_start: 0.7040 (t80) cc_final: 0.6009 (t80) REVERT: A 207 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7141 (t-90) REVERT: A 309 GLU cc_start: 0.7565 (pm20) cc_final: 0.7288 (pm20) REVERT: A 564 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7412 (mm-40) REVERT: A 581 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7584 (p) REVERT: A 670 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7554 (pt) REVERT: A 869 MET cc_start: 0.9022 (mtt) cc_final: 0.8745 (mtt) REVERT: A 1132 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 188 ASN cc_start: 0.6826 (m-40) cc_final: 0.6562 (p0) REVERT: B 342 PHE cc_start: 0.7874 (m-80) cc_final: 0.7647 (m-80) REVERT: B 347 PHE cc_start: 0.5814 (m-10) cc_final: 0.5530 (m-10) REVERT: B 355 ARG cc_start: 0.7241 (ttm170) cc_final: 0.6688 (tpp-160) REVERT: B 434 ILE cc_start: 0.5513 (OUTLIER) cc_final: 0.5216 (mt) REVERT: B 440 ASN cc_start: 0.7842 (m-40) cc_final: 0.7506 (p0) REVERT: B 581 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 740 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8307 (mmm) REVERT: C 202 LYS cc_start: 0.6885 (mtpt) cc_final: 0.6439 (mptt) REVERT: C 291 CYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6980 (m) REVERT: C 420 ASP cc_start: 0.6565 (m-30) cc_final: 0.6318 (t0) REVERT: C 495 TYR cc_start: 0.5875 (m-80) cc_final: 0.5022 (m-80) REVERT: C 528 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7221 (mmmm) REVERT: C 660 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6183 (p90) REVERT: C 671 CYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8232 (p) REVERT: C 740 MET cc_start: 0.8288 (ttt) cc_final: 0.7830 (ttm) REVERT: C 995 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7439 (mtt180) REVERT: P 3 MET cc_start: 0.3435 (tmm) cc_final: 0.3181 (tpt) REVERT: P 36 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6647 (mt) outliers start: 60 outliers final: 45 residues processed: 184 average time/residue: 0.9036 time to fit residues: 210.5988 Evaluate side-chains 184 residues out of total 2813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 2.898 ------------------------------------------------------------------------------- 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 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 1132 ILE 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 224 GLU 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 478 THR Chi-restraints excluded: chain B residue 514 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 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 740 MET 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 291 CYS Chi-restraints excluded: chain C residue 307 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 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 1104 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 47 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 146 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 262 optimal weight: 0.2980 chunk 189 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN P 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.175704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106338 restraints weight = 38281.217| |-----------------------------------------------------------------------------| 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: 0.3164 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2692 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= 0.167 Angle : 0.631 19.126 36272 Z= 0.313 Chirality : 0.047 0.394 4212 Planarity : 0.004 0.066 4615 Dihedral : 6.619 83.939 4434 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.11 % Rotamer: Outliers : 2.20 % Allowed : 14.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3176 helix: 2.00 (0.19), residues: 785 sheet: 0.17 (0.19), residues: 704 loop : -1.66 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.031 0.002 PHE h 33 TYR 0.035 0.002 TYR A 200 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 38) link_NAG-ASN : angle 3.07860 ( 114) link_BETA1-4 : bond 0.00388 ( 7) link_BETA1-4 : angle 1.10466 ( 21) hydrogen bonds : bond 0.05010 ( 989) hydrogen bonds : angle 5.07739 ( 2850) SS BOND : bond 0.00599 ( 37) SS BOND : angle 1.83311 ( 74) covalent geometry : bond 0.00405 (26518) covalent geometry : angle 0.60229 (36063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30912.29 seconds wall clock time: 532 minutes 38.78 seconds (31958.78 seconds total)