Starting phenix.real_space_refine on Fri Mar 6 01:01:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7enf_31209/03_2026/7enf_31209.cif Found real_map, /net/cci-nas-00/data/ceres_data/7enf_31209/03_2026/7enf_31209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7enf_31209/03_2026/7enf_31209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7enf_31209/03_2026/7enf_31209.map" model { file = "/net/cci-nas-00/data/ceres_data/7enf_31209/03_2026/7enf_31209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7enf_31209/03_2026/7enf_31209.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 116 5.16 5 C 16921 2.51 5 N 4353 2.21 5 O 5229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26619 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7393 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 8, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7746 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 7355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7355 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 52, 'TRANS': 923} Chain breaks: 12 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 205 Chain: "O" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "L" 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: "M" 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: "N" 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: "R" 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: "S" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.18, per 1000 atoms: 0.19 Number of scatterers: 26619 At special positions: 0 Unit cell: (130.353, 137.894, 224.078, 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 116 16.00 O 5229 8.00 N 4353 7.00 C 16921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.00 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.00 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.01 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 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 Simple disulfide: pdb=" SG CYS O 140 " - pdb=" SG CYS O 200 " distance=2.03 Simple disulfide: pdb=" SG CYS P 103 " - pdb=" SG CYS P 108 " distance=2.03 Simple disulfide: pdb=" SG CYS P 150 " - pdb=" SG CYS P 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " " NAG R 1 " - " ASN C 165 " " NAG S 1 " - " ASN B 343 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.2 seconds 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6360 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 53 sheets defined 23.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.570A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.802A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.511A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.659A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.557A 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 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.100A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.251A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.749A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 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: 3.817A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.876A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.676A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.549A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.514A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.024A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.836A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.672A 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.103A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 4.151A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.882A pdb=" N TYR C 160 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.646A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.900A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.137A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.519A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.264A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.775A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.582A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.563A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.127A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.856A 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 983 removed outlier: 3.578A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.087A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.643A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 134 removed outlier: 3.948A pdb=" N LEU O 131 " --> pdb=" O ASP O 128 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS O 132 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY O 134 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 193 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.572A pdb=" N SER P 31 " --> pdb=" O THR P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 65 Processing helix chain 'P' and resid 195 through 199 removed outlier: 3.630A pdb=" N LEU P 199 " --> pdb=" O SER P 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.582A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.767A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.909A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.024A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.234A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.310A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.844A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.942A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.372A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.655A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.007A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.195A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.758A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.894A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.356A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.177A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.508A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.103A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.701A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.980A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.518A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 567 through 568 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.275A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.872A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.985A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'O' and resid 12 through 13 Processing sheet with id=AF1, first strand: chain 'O' and resid 59 through 60 removed outlier: 6.433A pdb=" N TRP O 41 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR O 55 " --> pdb=" O LEU O 39 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU O 39 " --> pdb=" O TYR O 55 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 122 through 124 removed outlier: 6.141A pdb=" N TYR O 179 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 151 through 156 Processing sheet with id=AF4, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'P' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'P' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET P 34 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS P 96 " --> pdb=" O GLY P 114 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR P 112 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 132 through 134 Processing sheet with id=AF8, first strand: chain 'P' and resid 162 through 164 removed outlier: 3.647A pdb=" N SER P 163 " --> pdb=" O ASN P 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN P 207 " --> pdb=" O SER P 163 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR P 204 " --> pdb=" O VAL P 221 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4328 1.31 - 1.44: 7350 1.44 - 1.57: 15376 1.57 - 1.70: 0 1.70 - 1.83: 143 Bond restraints: 27197 Sorted by residual: bond pdb=" C7 NAG I 2 " pdb=" N2 NAG I 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG A1306 " pdb=" N2 NAG A1306 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C7 NAG I 1 " pdb=" N2 NAG I 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C7 NAG B1305 " pdb=" N2 NAG B1305 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 27192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 35834 2.45 - 4.89: 1027 4.89 - 7.34: 171 7.34 - 9.79: 35 9.79 - 12.23: 2 Bond angle restraints: 37069 Sorted by residual: angle pdb=" C CYS C 743 " pdb=" CA CYS C 743 " pdb=" CB CYS C 743 " ideal model delta sigma weight residual 111.85 99.62 12.23 1.47e+00 4.63e-01 6.93e+01 angle pdb=" N LEU B 517 " pdb=" CA LEU B 517 " pdb=" C LEU B 517 " ideal model delta sigma weight residual 113.21 105.35 7.86 1.15e+00 7.56e-01 4.67e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 112.17 121.11 -8.94 1.40e+00 5.10e-01 4.08e+01 angle pdb=" N SER O 33 " pdb=" CA SER O 33 " pdb=" C SER O 33 " ideal model delta sigma weight residual 111.28 105.03 6.25 1.09e+00 8.42e-01 3.29e+01 angle pdb=" N ASP A 138 " pdb=" CA ASP A 138 " pdb=" C ASP A 138 " ideal model delta sigma weight residual 108.75 99.35 9.40 1.70e+00 3.46e-01 3.06e+01 ... (remaining 37064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 15800 25.35 - 50.70: 729 50.70 - 76.06: 186 76.06 - 101.41: 100 101.41 - 126.76: 65 Dihedral angle restraints: 16880 sinusoidal: 7022 harmonic: 9858 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -174.06 88.06 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -6.53 -79.47 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.71 74.71 1 1.00e+01 1.00e-02 7.07e+01 ... (remaining 16877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3890 0.085 - 0.171: 489 0.171 - 0.256: 39 0.256 - 0.342: 12 0.342 - 0.427: 3 Chirality restraints: 4433 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.02e+01 chirality pdb=" CA TYR O 31 " pdb=" N TYR O 31 " pdb=" C TYR O 31 " pdb=" CB TYR O 31 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA CYS C 743 " pdb=" N CYS C 743 " pdb=" C CYS C 743 " pdb=" CB CYS C 743 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 4430 not shown) Planarity restraints: 4760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.332 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG R 2 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.516 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 741 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.83e+00 pdb=" C TYR C 741 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR C 741 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 742 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 31 " -0.031 2.00e-02 2.50e+03 2.01e-02 8.10e+00 pdb=" CG TYR O 31 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR O 31 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR O 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR O 31 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR O 31 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR O 31 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR O 31 " -0.005 2.00e-02 2.50e+03 ... (remaining 4757 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2044 2.73 - 3.28: 26337 3.28 - 3.82: 42561 3.82 - 4.36: 51571 4.36 - 4.90: 89517 Nonbonded interactions: 212030 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.197 3.040 nonbonded pdb=" O PHE P 29 " pdb=" NH2 ARG P 72 " model vdw 2.197 3.120 nonbonded pdb=" OD2 ASP C 40 " pdb=" NH1 ARG C 44 " model vdw 2.208 3.120 nonbonded pdb=" O PRO B1053 " pdb=" NE2 GLN B1054 " model vdw 2.208 3.120 ... (remaining 212025 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 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 243 or resid 264 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 350 or (resid 351 through 352 and (name N or name CA or na \ me C or name O or name CB )) or resid 353 through 363 or (resid 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 368 or (resid \ 369 and (name N or name CA or name C or name O or name CB )) or resid 370 throug \ h 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or \ resid 375 through 407 or (resid 408 and (name N or name CA or name C or name O o \ r name CB )) or resid 409 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 or (resid 449 and (name N or name CA o \ r name C or name O or name CB )) or resid 450 through 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 503 throug \ h 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) or \ resid 510 through 620 or resid 641 through 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 332 or (resid 333 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 through 339 or (resid 34 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 341 through \ 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or re \ sid 347 through 348 or (resid 349 and (name N or name CA or name C or name O or \ name CB )) or resid 350 or (resid 351 through 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 363 or (resid 364 and (name N or \ name CA or name C or name O or name CB )) or resid 365 through 368 or (resid 36 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 370 through \ 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or re \ sid 375 through 397 or (resid 398 and (name N or name CA or name C or name O or \ name CB )) or resid 399 through 402 or (resid 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 or (resid 405 through 408 and (name N or \ name CA or name C or name O or name CB )) or resid 409 through 413 or (resid 41 \ 4 through 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or re \ sid 418 through 419 or (resid 420 and (name N or name CA or name C or name O or \ name CB )) or resid 421 through 423 or (resid 424 and (name N or name CA or name \ C or name O or name CB )) or resid 425 through 426 or (resid 427 through 428 an \ d (name N or name CA or name C or name O or name CB )) or resid 429 through 440 \ or (resid 441 through 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 or (resid 449 and (name N or name CA or name C or name O or name \ CB )) or resid 450 through 453 or (resid 454 and (name N or name CA or name C o \ r name O or name CB )) or resid 491 or (resid 492 through 493 and (name N or nam \ e CA or name C or name O or name CB )) or resid 494 through 496 or (resid 497 th \ rough 498 and (name N or name CA or name C or name O or name CB )) or resid 503 \ through 508 or (resid 509 and (name N or name CA or name C or name O or name CB \ )) or resid 510 through 515 or (resid 516 and (name N or name CA or name C or na \ me O or name CB )) or resid 517 through 518 or (resid 519 through 520 and (name \ N or name CA or name C or name O or name CB )) or resid 521 through 527 or (resi \ d 528 through 529 and (name N or name CA or name C or name O or name CB )) or re \ sid 530 through 620 or resid 641 through 1307)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 454 or re \ sid 491 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.430 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.010 0.117 27289 Z= 0.488 Angle : 0.973 12.233 37306 Z= 0.518 Chirality : 0.058 0.427 4433 Planarity : 0.007 0.289 4720 Dihedral : 19.135 126.759 10403 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.53 % Allowed : 0.63 % Favored : 98.84 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3318 helix: 0.64 (0.21), residues: 667 sheet: -0.33 (0.17), residues: 838 loop : -1.85 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1039 TYR 0.047 0.002 TYR O 31 PHE 0.041 0.002 PHE B 906 TRP 0.024 0.002 TRP A 886 HIS 0.006 0.001 HIS O 204 Details of bonding type rmsd covalent geometry : bond 0.00972 (27197) covalent geometry : angle 0.95496 (37069) SS BOND : bond 0.00887 ( 39) SS BOND : angle 2.26353 ( 78) hydrogen bonds : bond 0.13933 ( 1091) hydrogen bonds : angle 7.28217 ( 2988) link_BETA1-4 : bond 0.00785 ( 13) link_BETA1-4 : angle 2.49786 ( 39) link_NAG-ASN : bond 0.00480 ( 40) link_NAG-ASN : angle 2.72543 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6346 (p90) cc_final: 0.5962 (p-80) REVERT: A 168 PHE cc_start: 0.7286 (t80) cc_final: 0.6741 (t80) REVERT: A 170 TYR cc_start: 0.8240 (t80) cc_final: 0.7857 (t80) REVERT: A 574 ASP cc_start: 0.7826 (t70) cc_final: 0.7593 (t0) REVERT: A 869 MET cc_start: 0.8826 (mtt) cc_final: 0.8456 (mtt) REVERT: B 118 LEU cc_start: 0.7743 (mm) cc_final: 0.7517 (mm) REVERT: B 129 LYS cc_start: 0.8666 (mppt) cc_final: 0.8416 (mppt) REVERT: B 342 PHE cc_start: 0.8828 (m-80) cc_final: 0.8625 (m-10) REVERT: B 358 ILE cc_start: 0.8531 (pt) cc_final: 0.8219 (pp) REVERT: B 403 ARG cc_start: 0.7566 (mtp180) cc_final: 0.7212 (mtp-110) REVERT: B 408 ARG cc_start: 0.8039 (ppt170) cc_final: 0.7637 (ppt170) REVERT: B 458 LYS cc_start: 0.8042 (pttp) cc_final: 0.7768 (tttt) REVERT: C 100 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7571 (mp) REVERT: C 133 PHE cc_start: 0.8592 (m-10) cc_final: 0.8212 (m-80) REVERT: C 174 PRO cc_start: 0.7294 (Cg_endo) cc_final: 0.6904 (Cg_exo) REVERT: O 95 HIS cc_start: 0.6500 (t70) cc_final: 0.5577 (t-90) REVERT: P 90 ASP cc_start: 0.3174 (OUTLIER) cc_final: 0.2544 (t70) outliers start: 15 outliers final: 4 residues processed: 217 average time/residue: 0.5271 time to fit residues: 136.7056 Evaluate side-chains 148 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain P residue 90 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 901 GLN A1010 GLN B 134 GLN B 394 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C 955 ASN C1002 GLN O 35 ASN P 57 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.156172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098862 restraints weight = 48625.919| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.57 r_work: 0.3191 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27289 Z= 0.158 Angle : 0.757 12.247 37306 Z= 0.360 Chirality : 0.050 0.311 4433 Planarity : 0.005 0.060 4720 Dihedral : 15.671 114.068 4714 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.88 % Allowed : 6.88 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3318 helix: 1.08 (0.21), residues: 686 sheet: -0.12 (0.17), residues: 863 loop : -1.68 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 319 TYR 0.025 0.002 TYR C 904 PHE 0.024 0.002 PHE B 92 TRP 0.013 0.001 TRP P 164 HIS 0.004 0.001 HIS O 204 Details of bonding type rmsd covalent geometry : bond 0.00364 (27197) covalent geometry : angle 0.73115 (37069) SS BOND : bond 0.00509 ( 39) SS BOND : angle 1.22946 ( 78) hydrogen bonds : bond 0.04821 ( 1091) hydrogen bonds : angle 6.12313 ( 2988) link_BETA1-4 : bond 0.00658 ( 13) link_BETA1-4 : angle 2.54690 ( 39) link_NAG-ASN : bond 0.00494 ( 40) link_NAG-ASN : angle 3.17995 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6403 (p90) cc_final: 0.5937 (p-80) REVERT: A 84 LEU cc_start: 0.6576 (mt) cc_final: 0.6270 (mt) REVERT: A 168 PHE cc_start: 0.7206 (t80) cc_final: 0.6541 (t80) REVERT: A 170 TYR cc_start: 0.8273 (t80) cc_final: 0.7897 (t80) REVERT: A 201 PHE cc_start: 0.7776 (t80) cc_final: 0.7564 (t80) REVERT: A 574 ASP cc_start: 0.7842 (t70) cc_final: 0.7553 (OUTLIER) REVERT: A 869 MET cc_start: 0.9037 (mtt) cc_final: 0.8750 (mtt) REVERT: B 52 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8457 (tp-100) REVERT: B 118 LEU cc_start: 0.7849 (mm) cc_final: 0.7586 (mt) REVERT: B 129 LYS cc_start: 0.8637 (mppt) cc_final: 0.8422 (mppt) REVERT: B 200 TYR cc_start: 0.8405 (m-80) cc_final: 0.8163 (m-80) REVERT: B 342 PHE cc_start: 0.8835 (m-80) cc_final: 0.8617 (m-10) REVERT: B 351 TYR cc_start: 0.8170 (t80) cc_final: 0.7899 (t80) REVERT: B 458 LYS cc_start: 0.8016 (pttp) cc_final: 0.7671 (tttt) REVERT: B 990 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 133 PHE cc_start: 0.8481 (m-10) cc_final: 0.8121 (m-80) REVERT: C 174 PRO cc_start: 0.7207 (Cg_endo) cc_final: 0.6785 (Cg_exo) REVERT: C 357 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8303 (mmm-85) REVERT: C 421 TYR cc_start: 0.5084 (OUTLIER) cc_final: 0.3789 (m-80) REVERT: O 95 HIS cc_start: 0.6222 (t70) cc_final: 0.5921 (t70) outliers start: 25 outliers final: 7 residues processed: 188 average time/residue: 0.5203 time to fit residues: 117.2558 Evaluate side-chains 154 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 747 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 227 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 173 optimal weight: 0.0070 chunk 330 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 213 optimal weight: 0.0980 overall best weight: 2.0204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 506 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 52 GLN P 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096863 restraints weight = 48580.771| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.33 r_work: 0.3175 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27289 Z= 0.209 Angle : 0.737 12.466 37306 Z= 0.352 Chirality : 0.050 0.284 4433 Planarity : 0.005 0.062 4720 Dihedral : 12.002 114.312 4710 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.73 % Allowed : 10.37 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3318 helix: 1.09 (0.21), residues: 691 sheet: 0.02 (0.17), residues: 860 loop : -1.64 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1107 TYR 0.033 0.002 TYR C 904 PHE 0.028 0.002 PHE B 906 TRP 0.026 0.002 TRP P 47 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00504 (27197) covalent geometry : angle 0.71167 (37069) SS BOND : bond 0.00396 ( 39) SS BOND : angle 1.23243 ( 78) hydrogen bonds : bond 0.05131 ( 1091) hydrogen bonds : angle 5.92430 ( 2988) link_BETA1-4 : bond 0.00608 ( 13) link_BETA1-4 : angle 2.42295 ( 39) link_NAG-ASN : bond 0.00463 ( 40) link_NAG-ASN : angle 3.05903 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6414 (p90) cc_final: 0.5938 (p-80) REVERT: A 84 LEU cc_start: 0.6479 (mt) cc_final: 0.6174 (mt) REVERT: A 168 PHE cc_start: 0.7181 (t80) cc_final: 0.6742 (t80) REVERT: A 170 TYR cc_start: 0.8348 (t80) cc_final: 0.7944 (t80) REVERT: A 574 ASP cc_start: 0.7906 (t70) cc_final: 0.7585 (OUTLIER) REVERT: A 869 MET cc_start: 0.9008 (mtt) cc_final: 0.8762 (mtt) REVERT: A 900 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8963 (mtp) REVERT: A 990 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 52 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8462 (tp-100) REVERT: B 118 LEU cc_start: 0.7803 (mm) cc_final: 0.7591 (mm) REVERT: B 129 LYS cc_start: 0.8685 (mppt) cc_final: 0.8440 (mppt) REVERT: B 170 TYR cc_start: 0.8124 (t80) cc_final: 0.7799 (t80) REVERT: B 200 TYR cc_start: 0.8417 (m-80) cc_final: 0.8167 (m-80) REVERT: B 207 HIS cc_start: 0.6780 (m-70) cc_final: 0.6442 (m-70) REVERT: B 269 TYR cc_start: 0.6775 (m-80) cc_final: 0.6480 (m-80) REVERT: B 342 PHE cc_start: 0.8858 (m-80) cc_final: 0.8618 (m-10) REVERT: B 458 LYS cc_start: 0.8117 (pttp) cc_final: 0.7713 (mmmt) REVERT: B 488 CYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3120 (m) REVERT: C 100 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7556 (mp) REVERT: C 133 PHE cc_start: 0.8483 (m-10) cc_final: 0.8180 (m-80) REVERT: C 174 PRO cc_start: 0.7109 (Cg_endo) cc_final: 0.6646 (Cg_exo) REVERT: C 319 ARG cc_start: 0.8269 (ttm110) cc_final: 0.7975 (ttp-170) REVERT: C 357 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8331 (mmm-85) REVERT: C 400 PHE cc_start: 0.7908 (p90) cc_final: 0.7692 (p90) REVERT: C 421 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.3775 (m-80) REVERT: C 614 ASP cc_start: 0.8469 (m-30) cc_final: 0.8002 (p0) REVERT: C 740 MET cc_start: 0.8751 (ttp) cc_final: 0.8416 (tpp) REVERT: O 95 HIS cc_start: 0.6211 (t70) cc_final: 0.5758 (t70) outliers start: 49 outliers final: 22 residues processed: 198 average time/residue: 0.4854 time to fit residues: 116.9236 Evaluate side-chains 176 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 291 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 330 optimal weight: 30.0000 chunk 180 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 580 GLN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.155003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096772 restraints weight = 48260.366| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.92 r_work: 0.3169 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27289 Z= 0.171 Angle : 0.695 12.549 37306 Z= 0.332 Chirality : 0.048 0.283 4433 Planarity : 0.005 0.061 4720 Dihedral : 10.398 111.753 4710 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.05 % Allowed : 11.99 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3318 helix: 1.27 (0.21), residues: 683 sheet: 0.05 (0.17), residues: 872 loop : -1.60 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 646 TYR 0.024 0.001 TYR B 904 PHE 0.018 0.001 PHE B 92 TRP 0.018 0.001 TRP P 47 HIS 0.004 0.001 HIS P 35 Details of bonding type rmsd covalent geometry : bond 0.00407 (27197) covalent geometry : angle 0.66903 (37069) SS BOND : bond 0.00328 ( 39) SS BOND : angle 1.17217 ( 78) hydrogen bonds : bond 0.04662 ( 1091) hydrogen bonds : angle 5.78084 ( 2988) link_BETA1-4 : bond 0.00600 ( 13) link_BETA1-4 : angle 2.38069 ( 39) link_NAG-ASN : bond 0.00409 ( 40) link_NAG-ASN : angle 3.02446 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 1.016 Fit side-chains REVERT: A 66 HIS cc_start: 0.6599 (p90) cc_final: 0.6116 (p-80) REVERT: A 84 LEU cc_start: 0.6344 (mt) cc_final: 0.6016 (mt) REVERT: A 168 PHE cc_start: 0.7285 (t80) cc_final: 0.6552 (t80) REVERT: A 170 TYR cc_start: 0.8357 (t80) cc_final: 0.7975 (t80) REVERT: A 574 ASP cc_start: 0.7850 (t70) cc_final: 0.7546 (OUTLIER) REVERT: A 869 MET cc_start: 0.9041 (mtt) cc_final: 0.8780 (mtt) REVERT: A 900 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8858 (mtp) REVERT: A 1040 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8835 (m) REVERT: B 118 LEU cc_start: 0.7707 (mm) cc_final: 0.7489 (mm) REVERT: B 129 LYS cc_start: 0.8690 (mppt) cc_final: 0.8423 (mppt) REVERT: B 200 TYR cc_start: 0.8400 (m-80) cc_final: 0.8118 (m-80) REVERT: B 207 HIS cc_start: 0.6816 (m-70) cc_final: 0.6426 (m-70) REVERT: B 269 TYR cc_start: 0.6789 (m-80) cc_final: 0.6510 (m-80) REVERT: B 342 PHE cc_start: 0.8848 (m-80) cc_final: 0.8607 (m-10) REVERT: B 365 TYR cc_start: 0.8406 (m-80) cc_final: 0.8137 (m-80) REVERT: B 403 ARG cc_start: 0.7683 (mtp180) cc_final: 0.6942 (mtp-110) REVERT: B 458 LYS cc_start: 0.8081 (pttp) cc_final: 0.7667 (mmmt) REVERT: B 490 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5549 (t80) REVERT: B 990 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7463 (tm-30) REVERT: C 133 PHE cc_start: 0.8467 (m-80) cc_final: 0.8223 (m-80) REVERT: C 174 PRO cc_start: 0.7064 (Cg_endo) cc_final: 0.6512 (Cg_exo) REVERT: C 226 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8321 (tt) REVERT: C 319 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7926 (ttp-170) REVERT: C 357 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8367 (mmm-85) REVERT: C 400 PHE cc_start: 0.7917 (p90) cc_final: 0.7686 (p90) REVERT: C 421 TYR cc_start: 0.4988 (OUTLIER) cc_final: 0.3501 (m-80) REVERT: C 614 ASP cc_start: 0.8456 (m-30) cc_final: 0.7998 (p0) REVERT: C 740 MET cc_start: 0.8645 (ttp) cc_final: 0.8320 (tpp) REVERT: O 95 HIS cc_start: 0.6189 (t70) cc_final: 0.5737 (t70) outliers start: 58 outliers final: 30 residues processed: 199 average time/residue: 0.4312 time to fit residues: 106.3280 Evaluate side-chains 181 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 179 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 122 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 334 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 9 optimal weight: 30.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.155397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097839 restraints weight = 48303.688| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.65 r_work: 0.3184 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27289 Z= 0.151 Angle : 0.663 12.510 37306 Z= 0.320 Chirality : 0.047 0.279 4433 Planarity : 0.004 0.060 4720 Dihedral : 9.236 109.861 4708 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.94 % Allowed : 13.01 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3318 helix: 1.35 (0.21), residues: 690 sheet: 0.20 (0.17), residues: 856 loop : -1.51 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.022 0.001 TYR B 904 PHE 0.016 0.001 PHE B 92 TRP 0.016 0.001 TRP P 47 HIS 0.003 0.001 HIS P 35 Details of bonding type rmsd covalent geometry : bond 0.00357 (27197) covalent geometry : angle 0.63670 (37069) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.32300 ( 78) hydrogen bonds : bond 0.04403 ( 1091) hydrogen bonds : angle 5.64810 ( 2988) link_BETA1-4 : bond 0.00586 ( 13) link_BETA1-4 : angle 2.45642 ( 39) link_NAG-ASN : bond 0.00381 ( 40) link_NAG-ASN : angle 2.89750 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.835 Fit side-chains REVERT: A 66 HIS cc_start: 0.6626 (p90) cc_final: 0.6132 (p-80) REVERT: A 84 LEU cc_start: 0.6430 (mt) cc_final: 0.6153 (mt) REVERT: A 168 PHE cc_start: 0.7141 (t80) cc_final: 0.6525 (t80) REVERT: A 170 TYR cc_start: 0.8327 (t80) cc_final: 0.7968 (t80) REVERT: A 574 ASP cc_start: 0.7700 (t70) cc_final: 0.7358 (OUTLIER) REVERT: A 869 MET cc_start: 0.8952 (mtt) cc_final: 0.8665 (mtt) REVERT: A 1040 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8817 (m) REVERT: B 118 LEU cc_start: 0.7736 (mm) cc_final: 0.7499 (mm) REVERT: B 129 LYS cc_start: 0.8714 (mppt) cc_final: 0.8432 (mppt) REVERT: B 200 TYR cc_start: 0.8324 (m-80) cc_final: 0.8015 (m-80) REVERT: B 269 TYR cc_start: 0.6743 (m-80) cc_final: 0.6431 (m-80) REVERT: B 342 PHE cc_start: 0.8833 (m-80) cc_final: 0.8562 (m-10) REVERT: B 403 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7412 (mtp-110) REVERT: B 458 LYS cc_start: 0.8117 (pttp) cc_final: 0.7669 (mmmt) REVERT: B 488 CYS cc_start: 0.4032 (OUTLIER) cc_final: 0.2994 (m) REVERT: B 490 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.5234 (t80) REVERT: B 990 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7472 (tm-30) REVERT: C 174 PRO cc_start: 0.6943 (Cg_endo) cc_final: 0.6472 (Cg_exo) REVERT: C 200 TYR cc_start: 0.7195 (m-80) cc_final: 0.6911 (t80) REVERT: C 206 LYS cc_start: 0.8904 (tttp) cc_final: 0.8613 (ttmm) REVERT: C 226 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 319 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7855 (ttp-170) REVERT: C 357 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8370 (mmm-85) REVERT: C 400 PHE cc_start: 0.7919 (p90) cc_final: 0.7702 (p90) REVERT: C 421 TYR cc_start: 0.4806 (OUTLIER) cc_final: 0.3351 (m-80) REVERT: C 614 ASP cc_start: 0.8313 (m-30) cc_final: 0.7944 (p0) REVERT: C 740 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8151 (tpp) REVERT: O 95 HIS cc_start: 0.6452 (t70) cc_final: 0.6064 (t70) REVERT: P 47 TRP cc_start: 0.7059 (t-100) cc_final: 0.6353 (t-100) REVERT: P 150 CYS cc_start: 0.2282 (OUTLIER) cc_final: 0.1826 (p) outliers start: 55 outliers final: 28 residues processed: 202 average time/residue: 0.4481 time to fit residues: 111.6505 Evaluate side-chains 182 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain P residue 150 CYS Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 316 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 159 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 150 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 751 ASN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN P 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.155990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098387 restraints weight = 48299.739| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.52 r_work: 0.3198 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27289 Z= 0.133 Angle : 0.646 12.978 37306 Z= 0.313 Chirality : 0.046 0.294 4433 Planarity : 0.004 0.058 4720 Dihedral : 8.585 109.765 4708 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.43 % Allowed : 13.54 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3318 helix: 1.49 (0.21), residues: 684 sheet: 0.29 (0.17), residues: 853 loop : -1.45 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 646 TYR 0.023 0.001 TYR B 904 PHE 0.022 0.001 PHE C 106 TRP 0.014 0.001 TRP O 41 HIS 0.002 0.000 HIS O 195 Details of bonding type rmsd covalent geometry : bond 0.00311 (27197) covalent geometry : angle 0.61903 (37069) SS BOND : bond 0.00500 ( 39) SS BOND : angle 1.53529 ( 78) hydrogen bonds : bond 0.04187 ( 1091) hydrogen bonds : angle 5.55465 ( 2988) link_BETA1-4 : bond 0.00545 ( 13) link_BETA1-4 : angle 2.47718 ( 39) link_NAG-ASN : bond 0.00356 ( 40) link_NAG-ASN : angle 2.83450 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 166 time to evaluate : 0.989 Fit side-chains REVERT: A 66 HIS cc_start: 0.6629 (p90) cc_final: 0.6136 (p-80) REVERT: A 84 LEU cc_start: 0.6471 (mt) cc_final: 0.6174 (mt) REVERT: A 168 PHE cc_start: 0.7151 (t80) cc_final: 0.6569 (t80) REVERT: A 170 TYR cc_start: 0.8333 (t80) cc_final: 0.7961 (t80) REVERT: A 574 ASP cc_start: 0.7777 (t70) cc_final: 0.7442 (OUTLIER) REVERT: A 869 MET cc_start: 0.9062 (mtt) cc_final: 0.8814 (mtt) REVERT: A 878 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8465 (mt) REVERT: A 990 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 1040 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8852 (m) REVERT: B 118 LEU cc_start: 0.7741 (mm) cc_final: 0.7480 (mm) REVERT: B 129 LYS cc_start: 0.8728 (mppt) cc_final: 0.8447 (mppt) REVERT: B 200 TYR cc_start: 0.8336 (m-80) cc_final: 0.8006 (m-80) REVERT: B 207 HIS cc_start: 0.7109 (m-70) cc_final: 0.6869 (m-70) REVERT: B 269 TYR cc_start: 0.6793 (m-80) cc_final: 0.6502 (m-80) REVERT: B 342 PHE cc_start: 0.8880 (m-80) cc_final: 0.8629 (m-10) REVERT: B 403 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7190 (mtp-110) REVERT: B 421 TYR cc_start: 0.7907 (m-80) cc_final: 0.7686 (m-80) REVERT: B 458 LYS cc_start: 0.8096 (pttp) cc_final: 0.7595 (mmmt) REVERT: B 488 CYS cc_start: 0.4021 (OUTLIER) cc_final: 0.2996 (m) REVERT: B 490 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.5092 (t80) REVERT: B 990 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 1141 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8030 (tp) REVERT: C 174 PRO cc_start: 0.6918 (Cg_endo) cc_final: 0.6448 (Cg_exo) REVERT: C 206 LYS cc_start: 0.8891 (tttp) cc_final: 0.8624 (ttmm) REVERT: C 226 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8287 (tt) REVERT: C 357 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8441 (mmm-85) REVERT: C 421 TYR cc_start: 0.4902 (OUTLIER) cc_final: 0.3329 (m-80) REVERT: C 614 ASP cc_start: 0.8437 (m-30) cc_final: 0.7994 (p0) REVERT: C 740 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8236 (tpp) REVERT: O 95 HIS cc_start: 0.6476 (t70) cc_final: 0.5977 (t70) REVERT: P 150 CYS cc_start: 0.2345 (OUTLIER) cc_final: 0.1522 (p) REVERT: P 196 SER cc_start: 0.1567 (OUTLIER) cc_final: 0.1291 (m) outliers start: 69 outliers final: 36 residues processed: 223 average time/residue: 0.4488 time to fit residues: 122.4011 Evaluate side-chains 191 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain P residue 150 CYS Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 288 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 202 optimal weight: 0.8980 chunk 316 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 309 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.155362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097571 restraints weight = 47900.365| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.54 r_work: 0.3211 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 27289 Z= 0.171 Angle : 0.671 18.991 37306 Z= 0.326 Chirality : 0.047 0.337 4433 Planarity : 0.004 0.057 4720 Dihedral : 8.313 109.552 4707 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.68 % Allowed : 14.21 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3318 helix: 1.45 (0.21), residues: 684 sheet: 0.27 (0.17), residues: 853 loop : -1.43 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 319 TYR 0.027 0.001 TYR B 904 PHE 0.025 0.001 PHE C 400 TRP 0.015 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00413 (27197) covalent geometry : angle 0.64313 (37069) SS BOND : bond 0.00555 ( 39) SS BOND : angle 1.75507 ( 78) hydrogen bonds : bond 0.04480 ( 1091) hydrogen bonds : angle 5.53922 ( 2988) link_BETA1-4 : bond 0.00504 ( 13) link_BETA1-4 : angle 2.46406 ( 39) link_NAG-ASN : bond 0.00353 ( 40) link_NAG-ASN : angle 2.84031 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 1.044 Fit side-chains REVERT: A 66 HIS cc_start: 0.6602 (p90) cc_final: 0.6125 (p-80) REVERT: A 84 LEU cc_start: 0.6560 (mt) cc_final: 0.6308 (mt) REVERT: A 168 PHE cc_start: 0.7307 (t80) cc_final: 0.6669 (t80) REVERT: A 170 TYR cc_start: 0.8364 (t80) cc_final: 0.8015 (t80) REVERT: A 574 ASP cc_start: 0.7768 (t70) cc_final: 0.7437 (OUTLIER) REVERT: A 869 MET cc_start: 0.9041 (mtt) cc_final: 0.8778 (mtt) REVERT: A 948 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 1040 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8851 (m) REVERT: B 118 LEU cc_start: 0.7774 (mm) cc_final: 0.7501 (mm) REVERT: B 129 LYS cc_start: 0.8743 (mppt) cc_final: 0.8456 (mppt) REVERT: B 200 TYR cc_start: 0.8343 (m-80) cc_final: 0.8053 (m-80) REVERT: B 207 HIS cc_start: 0.7125 (m-70) cc_final: 0.6898 (m-70) REVERT: B 269 TYR cc_start: 0.6842 (m-80) cc_final: 0.6556 (m-80) REVERT: B 342 PHE cc_start: 0.8910 (m-80) cc_final: 0.8654 (m-10) REVERT: B 403 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7207 (mtp-110) REVERT: B 421 TYR cc_start: 0.7895 (m-80) cc_final: 0.7675 (m-80) REVERT: B 458 LYS cc_start: 0.8095 (pttp) cc_final: 0.7573 (mmmt) REVERT: B 488 CYS cc_start: 0.4037 (OUTLIER) cc_final: 0.2995 (m) REVERT: B 490 PHE cc_start: 0.5726 (OUTLIER) cc_final: 0.5058 (t80) REVERT: B 990 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 1141 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8027 (tp) REVERT: C 133 PHE cc_start: 0.8390 (m-80) cc_final: 0.7390 (t80) REVERT: C 171 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8460 (p) REVERT: C 174 PRO cc_start: 0.6955 (Cg_endo) cc_final: 0.6485 (Cg_exo) REVERT: C 226 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8400 (tt) REVERT: C 319 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7747 (ttp-170) REVERT: C 357 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8495 (mmm-85) REVERT: C 400 PHE cc_start: 0.7919 (p90) cc_final: 0.7703 (p90) REVERT: C 421 TYR cc_start: 0.4788 (OUTLIER) cc_final: 0.3207 (m-80) REVERT: C 614 ASP cc_start: 0.8411 (m-30) cc_final: 0.7994 (p0) REVERT: C 646 ARG cc_start: 0.8515 (mpp80) cc_final: 0.8286 (mpp80) REVERT: C 740 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8297 (tpp) REVERT: O 95 HIS cc_start: 0.6523 (t70) cc_final: 0.6015 (t70) REVERT: P 150 CYS cc_start: 0.2230 (OUTLIER) cc_final: 0.1353 (p) outliers start: 76 outliers final: 41 residues processed: 219 average time/residue: 0.4383 time to fit residues: 118.5528 Evaluate side-chains 197 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 150 CYS Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 125 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 158 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 172 GLN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.155749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098293 restraints weight = 48533.864| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.52 r_work: 0.3197 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27289 Z= 0.144 Angle : 0.651 16.949 37306 Z= 0.317 Chirality : 0.047 0.311 4433 Planarity : 0.004 0.057 4720 Dihedral : 8.036 109.441 4707 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.26 % Allowed : 14.88 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3318 helix: 1.50 (0.21), residues: 683 sheet: 0.31 (0.17), residues: 858 loop : -1.40 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1019 TYR 0.025 0.001 TYR B 904 PHE 0.023 0.001 PHE C 106 TRP 0.013 0.001 TRP O 56 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00343 (27197) covalent geometry : angle 0.62458 (37069) SS BOND : bond 0.00541 ( 39) SS BOND : angle 1.51260 ( 78) hydrogen bonds : bond 0.04251 ( 1091) hydrogen bonds : angle 5.48425 ( 2988) link_BETA1-4 : bond 0.00494 ( 13) link_BETA1-4 : angle 2.41155 ( 39) link_NAG-ASN : bond 0.00353 ( 40) link_NAG-ASN : angle 2.79693 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 157 time to evaluate : 0.960 Fit side-chains REVERT: A 66 HIS cc_start: 0.6592 (p90) cc_final: 0.6115 (p-80) REVERT: A 84 LEU cc_start: 0.6823 (mt) cc_final: 0.6581 (mt) REVERT: A 168 PHE cc_start: 0.7248 (t80) cc_final: 0.6589 (t80) REVERT: A 170 TYR cc_start: 0.8358 (t80) cc_final: 0.7951 (t80) REVERT: A 574 ASP cc_start: 0.7759 (t70) cc_final: 0.7421 (OUTLIER) REVERT: A 869 MET cc_start: 0.9051 (mtt) cc_final: 0.8796 (mtt) REVERT: A 948 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 1040 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8850 (m) REVERT: B 118 LEU cc_start: 0.7756 (mm) cc_final: 0.7471 (mm) REVERT: B 129 LYS cc_start: 0.8702 (mppt) cc_final: 0.8416 (mppt) REVERT: B 157 PHE cc_start: 0.8007 (p90) cc_final: 0.7785 (p90) REVERT: B 200 TYR cc_start: 0.8326 (m-80) cc_final: 0.8003 (m-80) REVERT: B 207 HIS cc_start: 0.6996 (m-70) cc_final: 0.6734 (m-70) REVERT: B 269 TYR cc_start: 0.6801 (m-80) cc_final: 0.6511 (m-80) REVERT: B 342 PHE cc_start: 0.8899 (m-80) cc_final: 0.8621 (m-10) REVERT: B 403 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7150 (mtp-110) REVERT: B 421 TYR cc_start: 0.7914 (m-80) cc_final: 0.7696 (m-80) REVERT: B 458 LYS cc_start: 0.8003 (pttp) cc_final: 0.7525 (mmmt) REVERT: B 488 CYS cc_start: 0.3881 (OUTLIER) cc_final: 0.2892 (m) REVERT: B 490 PHE cc_start: 0.5730 (OUTLIER) cc_final: 0.5048 (t80) REVERT: B 990 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 1141 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8010 (tp) REVERT: C 133 PHE cc_start: 0.8407 (m-80) cc_final: 0.7464 (t80) REVERT: C 174 PRO cc_start: 0.6920 (Cg_endo) cc_final: 0.6448 (Cg_exo) REVERT: C 319 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7756 (ttp-170) REVERT: C 357 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8502 (mmm-85) REVERT: C 421 TYR cc_start: 0.4781 (OUTLIER) cc_final: 0.3292 (m-80) REVERT: C 614 ASP cc_start: 0.8426 (m-30) cc_final: 0.8003 (p0) REVERT: C 646 ARG cc_start: 0.8507 (mpp80) cc_final: 0.8306 (mpp80) REVERT: C 740 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8246 (tpp) REVERT: C 745 ASP cc_start: 0.8227 (t0) cc_final: 0.7858 (t0) REVERT: C 1138 TYR cc_start: 0.8086 (m-80) cc_final: 0.7693 (t80) REVERT: O 95 HIS cc_start: 0.6437 (t70) cc_final: 0.5987 (t70) REVERT: P 150 CYS cc_start: 0.2489 (OUTLIER) cc_final: 0.1686 (p) outliers start: 64 outliers final: 38 residues processed: 206 average time/residue: 0.4053 time to fit residues: 104.7106 Evaluate side-chains 197 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 150 CYS Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 37 optimal weight: 30.0000 chunk 304 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 263 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.155713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096031 restraints weight = 48436.010| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.31 r_work: 0.3182 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27289 Z= 0.149 Angle : 0.665 15.884 37306 Z= 0.324 Chirality : 0.047 0.291 4433 Planarity : 0.004 0.056 4720 Dihedral : 7.901 113.140 4706 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.08 % Allowed : 15.30 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3318 helix: 1.50 (0.21), residues: 683 sheet: 0.29 (0.17), residues: 873 loop : -1.39 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.025 0.001 TYR C 380 PHE 0.014 0.001 PHE A 643 TRP 0.017 0.001 TRP O 56 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00361 (27197) covalent geometry : angle 0.63693 (37069) SS BOND : bond 0.00443 ( 39) SS BOND : angle 2.00989 ( 78) hydrogen bonds : bond 0.04302 ( 1091) hydrogen bonds : angle 5.48789 ( 2988) link_BETA1-4 : bond 0.00478 ( 13) link_BETA1-4 : angle 2.35948 ( 39) link_NAG-ASN : bond 0.00342 ( 40) link_NAG-ASN : angle 2.76162 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 157 time to evaluate : 1.055 Fit side-chains REVERT: A 66 HIS cc_start: 0.6598 (p90) cc_final: 0.6128 (p-80) REVERT: A 84 LEU cc_start: 0.6721 (mt) cc_final: 0.6461 (mt) REVERT: A 168 PHE cc_start: 0.7219 (t80) cc_final: 0.6565 (t80) REVERT: A 170 TYR cc_start: 0.8353 (t80) cc_final: 0.7935 (t80) REVERT: A 574 ASP cc_start: 0.7727 (t70) cc_final: 0.7385 (OUTLIER) REVERT: A 869 MET cc_start: 0.9034 (mtt) cc_final: 0.8772 (mtt) REVERT: A 948 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8856 (mp) REVERT: A 1040 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8839 (m) REVERT: B 118 LEU cc_start: 0.7728 (mm) cc_final: 0.7433 (mm) REVERT: B 129 LYS cc_start: 0.8674 (mppt) cc_final: 0.8390 (mppt) REVERT: B 157 PHE cc_start: 0.8120 (p90) cc_final: 0.7803 (p90) REVERT: B 200 TYR cc_start: 0.8306 (m-80) cc_final: 0.7991 (m-80) REVERT: B 207 HIS cc_start: 0.6969 (m-70) cc_final: 0.6715 (m-70) REVERT: B 269 TYR cc_start: 0.6764 (m-80) cc_final: 0.6463 (m-80) REVERT: B 342 PHE cc_start: 0.8880 (m-80) cc_final: 0.8553 (m-10) REVERT: B 403 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7129 (mtp-110) REVERT: B 408 ARG cc_start: 0.7857 (ptm-80) cc_final: 0.7523 (pmt-80) REVERT: B 458 LYS cc_start: 0.8003 (pttp) cc_final: 0.7521 (mmmt) REVERT: B 488 CYS cc_start: 0.3827 (OUTLIER) cc_final: 0.2846 (m) REVERT: B 490 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.4889 (t80) REVERT: B 990 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 1141 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7992 (tp) REVERT: C 133 PHE cc_start: 0.8424 (m-80) cc_final: 0.7487 (t80) REVERT: C 174 PRO cc_start: 0.6852 (Cg_endo) cc_final: 0.6372 (Cg_exo) REVERT: C 188 ASN cc_start: 0.7540 (p0) cc_final: 0.6719 (m110) REVERT: C 319 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7798 (ttp-170) REVERT: C 357 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8449 (mmm-85) REVERT: C 421 TYR cc_start: 0.4857 (OUTLIER) cc_final: 0.3277 (m-80) REVERT: C 614 ASP cc_start: 0.8413 (m-30) cc_final: 0.7990 (p0) REVERT: C 740 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8207 (tpp) REVERT: C 745 ASP cc_start: 0.8240 (t0) cc_final: 0.7890 (t0) REVERT: C 1138 TYR cc_start: 0.8058 (m-80) cc_final: 0.7672 (t80) REVERT: O 95 HIS cc_start: 0.6341 (t70) cc_final: 0.5928 (t70) REVERT: P 150 CYS cc_start: 0.2469 (OUTLIER) cc_final: 0.1658 (p) outliers start: 59 outliers final: 39 residues processed: 202 average time/residue: 0.4344 time to fit residues: 109.2110 Evaluate side-chains 198 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 150 CYS Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 148 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 331 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 322 optimal weight: 20.0000 chunk 236 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.155030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097265 restraints weight = 48246.962| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.71 r_work: 0.3201 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 27289 Z= 0.189 Angle : 0.684 15.485 37306 Z= 0.333 Chirality : 0.048 0.547 4433 Planarity : 0.004 0.056 4720 Dihedral : 7.615 111.888 4706 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.83 % Allowed : 15.66 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3318 helix: 1.52 (0.21), residues: 671 sheet: 0.29 (0.17), residues: 867 loop : -1.42 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.028 0.001 TYR C 380 PHE 0.024 0.001 PHE C 106 TRP 0.015 0.002 TRP O 56 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00461 (27197) covalent geometry : angle 0.65430 (37069) SS BOND : bond 0.00458 ( 39) SS BOND : angle 1.96508 ( 78) hydrogen bonds : bond 0.04654 ( 1091) hydrogen bonds : angle 5.51776 ( 2988) link_BETA1-4 : bond 0.00398 ( 13) link_BETA1-4 : angle 2.44847 ( 39) link_NAG-ASN : bond 0.00523 ( 40) link_NAG-ASN : angle 2.98334 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 1.118 Fit side-chains REVERT: A 66 HIS cc_start: 0.6607 (p90) cc_final: 0.6148 (p-80) REVERT: A 84 LEU cc_start: 0.6789 (mt) cc_final: 0.6506 (mt) REVERT: A 168 PHE cc_start: 0.7180 (t80) cc_final: 0.6564 (t80) REVERT: A 170 TYR cc_start: 0.8357 (t80) cc_final: 0.7942 (t80) REVERT: A 574 ASP cc_start: 0.7764 (t70) cc_final: 0.7410 (OUTLIER) REVERT: A 948 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8869 (mp) REVERT: A 1040 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8827 (m) REVERT: B 66 HIS cc_start: 0.4098 (OUTLIER) cc_final: 0.3738 (t-90) REVERT: B 118 LEU cc_start: 0.7763 (mm) cc_final: 0.7477 (mm) REVERT: B 129 LYS cc_start: 0.8659 (mppt) cc_final: 0.8357 (mppt) REVERT: B 157 PHE cc_start: 0.8099 (p90) cc_final: 0.7824 (p90) REVERT: B 200 TYR cc_start: 0.8341 (m-80) cc_final: 0.7993 (m-80) REVERT: B 207 HIS cc_start: 0.6917 (m-70) cc_final: 0.6670 (m-70) REVERT: B 269 TYR cc_start: 0.6855 (m-80) cc_final: 0.6567 (m-80) REVERT: B 403 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7250 (mtp-110) REVERT: B 421 TYR cc_start: 0.7625 (m-80) cc_final: 0.7323 (m-80) REVERT: B 458 LYS cc_start: 0.8021 (pttp) cc_final: 0.7508 (mmmt) REVERT: B 488 CYS cc_start: 0.3839 (OUTLIER) cc_final: 0.2810 (m) REVERT: B 490 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.4880 (t80) REVERT: B 990 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 1141 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8017 (tp) REVERT: C 133 PHE cc_start: 0.8443 (m-80) cc_final: 0.7528 (t80) REVERT: C 174 PRO cc_start: 0.6895 (Cg_endo) cc_final: 0.6457 (Cg_exo) REVERT: C 188 ASN cc_start: 0.7531 (p0) cc_final: 0.6721 (m110) REVERT: C 206 LYS cc_start: 0.8892 (tttp) cc_final: 0.8654 (ttmm) REVERT: C 319 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7800 (ttp-170) REVERT: C 357 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8533 (mmm-85) REVERT: C 421 TYR cc_start: 0.4974 (OUTLIER) cc_final: 0.3236 (m-80) REVERT: C 614 ASP cc_start: 0.8425 (m-30) cc_final: 0.8003 (p0) REVERT: C 740 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8309 (tpp) REVERT: O 95 HIS cc_start: 0.6465 (t70) cc_final: 0.6049 (t70) REVERT: P 47 TRP cc_start: 0.6651 (t-100) cc_final: 0.6375 (t-100) REVERT: P 150 CYS cc_start: 0.2485 (OUTLIER) cc_final: 0.1688 (p) outliers start: 52 outliers final: 36 residues processed: 193 average time/residue: 0.4152 time to fit residues: 99.3019 Evaluate side-chains 195 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 150 CYS Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 38 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 158 optimal weight: 0.0770 chunk 300 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN P 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.155063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090796 restraints weight = 48068.251| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.63 r_work: 0.3190 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 27289 Z= 0.189 Angle : 0.679 15.183 37306 Z= 0.332 Chirality : 0.048 0.480 4433 Planarity : 0.004 0.055 4720 Dihedral : 7.542 112.067 4706 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.83 % Allowed : 15.94 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3318 helix: 1.46 (0.21), residues: 677 sheet: 0.28 (0.17), residues: 868 loop : -1.40 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.028 0.001 TYR B 904 PHE 0.030 0.001 PHE B 497 TRP 0.014 0.001 TRP O 56 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00459 (27197) covalent geometry : angle 0.64977 (37069) SS BOND : bond 0.00458 ( 39) SS BOND : angle 1.88475 ( 78) hydrogen bonds : bond 0.04651 ( 1091) hydrogen bonds : angle 5.51696 ( 2988) link_BETA1-4 : bond 0.00423 ( 13) link_BETA1-4 : angle 2.42464 ( 39) link_NAG-ASN : bond 0.00400 ( 40) link_NAG-ASN : angle 2.91717 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12334.72 seconds wall clock time: 209 minutes 39.83 seconds (12579.83 seconds total)