Starting phenix.real_space_refine on Sun Jul 5 07:55:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3q_62788/07_2026/9l3q_62788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3q_62788/07_2026/9l3q_62788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l3q_62788/07_2026/9l3q_62788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3q_62788/07_2026/9l3q_62788.map" model { file = "/net/cci-nas-00/data/ceres_data/9l3q_62788/07_2026/9l3q_62788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3q_62788/07_2026/9l3q_62788.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 16392 2.51 5 N 4211 2.21 5 O 5028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25747 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8345 Classifications: {'peptide': 1067} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8336 Classifications: {'peptide': 1067} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8029 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 102 Classifications: {'peptide': 13} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'28J:plan-1': 1, 'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 102 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'28J:plan-1': 1, 'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 102 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'28J:plan-1': 1, 'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: "O" 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: "P" 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: "Q" 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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: "C" 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 Time building chain proxies: 6.96, per 1000 atoms: 0.27 Number of scatterers: 25747 At special positions: 0 Unit cell: (146.91, 165.17, 179.28, 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 5028 8.00 N 4211 7.00 C 16392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=6, 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 149 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG D 1 " - " ASN A 149 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 17 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 17 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 28J T 4 " pdb=" CB 28J U 4 " pdb=" CB 28J V 4 " Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 49 sheets defined 24.8% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.652A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.615A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.338A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.964A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.507A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) 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 761 through 783 removed outlier: 3.630A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.517A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.194A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.724A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.677A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.933A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.613A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.612A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.636A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.988A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.635A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) 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 760 through 783 removed outlier: 3.645A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.334A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.907A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.844A 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 removed outlier: 3.661A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.892A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.041A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.681A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.563A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.254A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.561A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.605A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.858A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.516A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.756A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.236A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.535A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.947A 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.963A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'V' and resid 4 through 9 removed outlier: 3.582A pdb=" N LEU V 8 " --> pdb=" O 28J V 4 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.140A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.140A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.130A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.764A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.601A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.672A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.501A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.543A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.933A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.647A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.893A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.618A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.171A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.535A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.031A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.534A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.031A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.454A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.808A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.052A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.510A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.992A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.699A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.078A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.535A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.674A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.711A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.676A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.490A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.028A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.227A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.189A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.581A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.002A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.528A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 2868 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: 6.32 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4479 1.33 - 1.45: 7380 1.45 - 1.58: 14326 1.58 - 1.71: 0 1.71 - 1.83: 148 Bond restraints: 26333 Sorted by residual: bond pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta sigma weight residual 1.458 1.499 -0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" CA SER A 375 " pdb=" CB SER A 375 " ideal model delta sigma weight residual 1.536 1.483 0.052 1.53e-02 4.27e+03 1.18e+01 bond pdb=" N CYS A 432 " pdb=" CA CYS A 432 " ideal model delta sigma weight residual 1.454 1.494 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" CA SER A 383 " pdb=" CB SER A 383 " ideal model delta sigma weight residual 1.535 1.471 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N VAL C 433 " pdb=" CA VAL C 433 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.00e+01 ... (remaining 26328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 34596 1.77 - 3.54: 1082 3.54 - 5.31: 144 5.31 - 7.08: 18 7.08 - 8.86: 5 Bond angle restraints: 35845 Sorted by residual: angle pdb=" C THR A 376 " pdb=" CA THR A 376 " pdb=" CB THR A 376 " ideal model delta sigma weight residual 110.62 119.22 -8.60 1.46e+00 4.69e-01 3.47e+01 angle pdb=" N PRO A 527 " pdb=" CA PRO A 527 " pdb=" CB PRO A 527 " ideal model delta sigma weight residual 102.65 99.00 3.65 6.80e-01 2.16e+00 2.88e+01 angle pdb=" CA VAL B 433 " pdb=" C VAL B 433 " pdb=" N ILE B 434 " ideal model delta sigma weight residual 116.51 121.57 -5.06 1.07e+00 8.73e-01 2.24e+01 angle pdb=" CA VAL B 433 " pdb=" C VAL B 433 " pdb=" O VAL B 433 " ideal model delta sigma weight residual 120.27 115.72 4.55 1.01e+00 9.80e-01 2.03e+01 angle pdb=" N THR B 761 " pdb=" CA THR B 761 " pdb=" C THR B 761 " ideal model delta sigma weight residual 111.82 106.89 4.93 1.16e+00 7.43e-01 1.81e+01 ... (remaining 35840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.72: 15001 19.72 - 39.44: 1148 39.44 - 59.16: 178 59.16 - 78.87: 50 78.87 - 98.59: 16 Dihedral angle restraints: 16393 sinusoidal: 7091 harmonic: 9302 Sorted by residual: dihedral pdb=" CA THR U 6 " pdb=" C THR U 6 " pdb=" N PRO U 7 " pdb=" CA PRO U 7 " ideal model delta harmonic sigma weight residual 180.00 81.41 98.59 0 5.00e+00 4.00e-02 3.89e+02 dihedral pdb=" CA THR V 6 " pdb=" C THR V 6 " pdb=" N PRO V 7 " pdb=" CA PRO V 7 " ideal model delta harmonic sigma weight residual 180.00 96.24 83.76 0 5.00e+00 4.00e-02 2.81e+02 dihedral pdb=" CA CCS U 12 " pdb=" C CCS U 12 " pdb=" N GLY U 13 " pdb=" CA GLY U 13 " ideal model delta harmonic sigma weight residual 180.00 113.12 66.88 0 5.00e+00 4.00e-02 1.79e+02 ... (remaining 16390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3469 0.061 - 0.122: 659 0.122 - 0.183: 65 0.183 - 0.243: 10 0.243 - 0.304: 2 Chirality restraints: 4205 Sorted by residual: chirality pdb=" CB VAL A 524 " pdb=" CA VAL A 524 " pdb=" CG1 VAL A 524 " pdb=" CG2 VAL A 524 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB VAL B 382 " pdb=" CA VAL B 382 " pdb=" CG1 VAL B 382 " pdb=" CG2 VAL B 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA VAL C 382 " pdb=" N VAL C 382 " pdb=" C VAL C 382 " pdb=" CB VAL C 382 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4202 not shown) Planarity restraints: 4618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 430 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C THR C 430 " -0.074 2.00e-02 2.50e+03 pdb=" O THR C 430 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY C 431 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 430 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C THR B 430 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 430 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 431 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 561 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.048 5.00e-02 4.00e+02 ... (remaining 4615 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1188 2.72 - 3.27: 24051 3.27 - 3.81: 39015 3.81 - 4.36: 46993 4.36 - 4.90: 83918 Nonbonded interactions: 195165 Sorted by model distance: nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 2.181 3.120 nonbonded pdb=" O SER A 116 " pdb=" N CYS A 131 " model vdw 2.199 3.120 nonbonded pdb=" O GLY B 908 " pdb=" NZ LYS B1038 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.227 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.229 3.040 ... (remaining 195160 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 14 through 66 or resid 80 through 121 or resid 126 through \ 171 or resid 186 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 213 or (resid 214 and (name N or name \ CA or name C or name O or name CB )) or resid 215 through 243 or resid 263 throu \ gh 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) or \ resid 559 through 1044 or (resid 1045 and (name N or name CA or name C or name \ O or name CB )) or resid 1046 through 1307)) selection = (chain 'B' and (resid 14 through 66 or resid 80 through 121 or resid 126 through \ 129 or resid 131 through 171 or resid 186 through 190 or (resid 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 243 or resid \ 263 through 515 or (resid 516 and (name N or name CA or name C or name O or name \ CB )) or resid 517 through 827 or resid 855 through 1044 or (resid 1045 and (na \ me N or name CA or name C or name O or name CB )) or resid 1046 through 1307)) selection = (chain 'C' and (resid 14 through 129 or resid 131 through 213 or (resid 214 and \ (name N or name CA or name C or name O or name CB )) or resid 215 through 515 or \ (resid 516 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 7 through 557 or (resid 558 and (name N or name CA or name C or name O or name C \ B )) or resid 559 through 827 or resid 855 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 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 12.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.310 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 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:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 26433 Z= 0.264 Angle : 0.718 8.855 36085 Z= 0.396 Chirality : 0.048 0.304 4205 Planarity : 0.005 0.089 4581 Dihedral : 13.839 98.593 10285 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.43 % Favored : 95.41 % Rotamer: Outliers : 0.64 % Allowed : 0.36 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.37 % 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: -0.05 (0.15), residues: 3140 helix: 1.85 (0.21), residues: 682 sheet: 1.15 (0.18), residues: 718 loop : -1.42 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 158 TYR 0.026 0.001 TYR A 495 PHE 0.017 0.001 PHE B 906 TRP 0.016 0.001 TRP A 258 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 (26333) covalent geometry : angle 0.69664 / 0.39 (35845) SS BOND : bond 0.00457 / 0.30 ( 42) SS BOND : angle 2.46105 / 1.84 ( 84) hydrogen bonds : bond 0.12818 / 8.30 ( 1023) hydrogen bonds : angle 5.97511 / 4.11 ( 2868) Misc. bond : bond 0.10170 / 5.31 ( 6) link_BETA1-4 : bond 0.00431 / 0.25 ( 15) link_BETA1-4 : angle 1.47850 / 0.92 ( 45) link_NAG-ASN : bond 0.00357 / 0.24 ( 37) link_NAG-ASN : angle 2.35202 / 1.67 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 619 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.7730 (m) cc_final: 0.7376 (t) REVERT: A 138 ASP cc_start: 0.7791 (t70) cc_final: 0.7229 (t0) REVERT: A 414 GLN cc_start: 0.8360 (mm110) cc_final: 0.8157 (mp10) REVERT: A 465 GLU cc_start: 0.7506 (tp30) cc_final: 0.7287 (tp30) REVERT: A 675 GLN cc_start: 0.7669 (pp30) cc_final: 0.7403 (pp30) REVERT: A 1017 GLU cc_start: 0.7267 (tp30) cc_final: 0.6857 (tp30) REVERT: B 158 ARG cc_start: 0.8345 (mtt90) cc_final: 0.8119 (mtt90) REVERT: B 178 ASP cc_start: 0.7886 (t0) cc_final: 0.7484 (t0) REVERT: B 420 ASP cc_start: 0.7487 (m-30) cc_final: 0.7228 (m-30) REVERT: B 574 ASP cc_start: 0.7779 (t0) cc_final: 0.7451 (t0) REVERT: B 583 GLU cc_start: 0.7284 (tt0) cc_final: 0.6756 (tt0) REVERT: B 586 ASP cc_start: 0.7440 (m-30) cc_final: 0.7220 (m-30) REVERT: B 776 LYS cc_start: 0.8426 (tttp) cc_final: 0.8225 (tttm) REVERT: B 819 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 969 ASN cc_start: 0.8552 (m110) cc_final: 0.8342 (m-40) REVERT: B 1094 VAL cc_start: 0.8899 (m) cc_final: 0.8608 (p) REVERT: C 169 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6967 (tm-30) REVERT: C 281 GLU cc_start: 0.7592 (mp0) cc_final: 0.7306 (mp0) REVERT: C 309 GLU cc_start: 0.7586 (mp0) cc_final: 0.7200 (mp0) REVERT: C 377 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7336 (p90) REVERT: C 583 GLU cc_start: 0.7705 (tt0) cc_final: 0.7416 (tt0) REVERT: C 1010 GLN cc_start: 0.8271 (mm110) cc_final: 0.8068 (mm110) outliers start: 18 outliers final: 8 residues processed: 630 average time/residue: 0.5662 time to fit residues: 412.3984 Evaluate side-chains 592 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 583 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 11 LYS Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN A 777 ASN A 804 GLN A 969 ASN A1119 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 196 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 949 GLN B1010 GLN B1119 ASN C 30 ASN C 501 ASN C 777 ASN C 907 ASN C1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.125520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108934 restraints weight = 39419.534| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.31 r_work: 0.3358 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26433 Z= 0.176 Angle : 0.644 9.458 36085 Z= 0.326 Chirality : 0.047 0.264 4205 Planarity : 0.005 0.071 4581 Dihedral : 7.601 61.109 4567 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 1.93 % Allowed : 10.04 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3140 helix: 2.07 (0.21), residues: 676 sheet: 1.23 (0.18), residues: 696 loop : -1.39 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 995 TYR 0.022 0.002 TYR A 265 PHE 0.017 0.002 PHE B 157 TRP 0.010 0.001 TRP A 436 HIS 0.011 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (26333) covalent geometry : angle 0.62583 / 0.32 (35845) SS BOND : bond 0.00551 / 0.38 ( 42) SS BOND : angle 2.02529 / 1.45 ( 84) hydrogen bonds : bond 0.06229 / 4.18 ( 1023) hydrogen bonds : angle 5.08843 / 3.49 ( 2868) Misc. bond : bond 0.00169 / 0.08 ( 6) link_BETA1-4 : bond 0.00409 / 0.25 ( 15) link_BETA1-4 : angle 1.28531 / 0.80 ( 45) link_NAG-ASN : bond 0.00323 / 0.21 ( 37) link_NAG-ASN : angle 2.11953 / 1.46 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 621 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.7991 (m) cc_final: 0.7583 (t) REVERT: A 408 ARG cc_start: 0.8663 (ptm-80) cc_final: 0.8147 (ptm-80) REVERT: A 414 GLN cc_start: 0.8571 (mm110) cc_final: 0.8334 (mp10) REVERT: A 465 GLU cc_start: 0.7698 (tp30) cc_final: 0.7427 (tp30) REVERT: A 675 GLN cc_start: 0.7902 (pp30) cc_final: 0.7497 (pp30) REVERT: A 933 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8222 (mtmt) REVERT: A 1017 GLU cc_start: 0.7825 (tp30) cc_final: 0.7367 (tp30) REVERT: B 97 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7880 (ptpp) REVERT: B 178 ASP cc_start: 0.8143 (t0) cc_final: 0.7710 (t0) REVERT: B 200 TYR cc_start: 0.8028 (m-10) cc_final: 0.7719 (m-80) REVERT: B 228 ASP cc_start: 0.6976 (t0) cc_final: 0.6481 (t70) REVERT: B 354 ASN cc_start: 0.8166 (t0) cc_final: 0.7899 (t0) REVERT: B 364 ASP cc_start: 0.7460 (t0) cc_final: 0.7230 (t0) REVERT: B 420 ASP cc_start: 0.7840 (m-30) cc_final: 0.7594 (m-30) REVERT: B 534 VAL cc_start: 0.8551 (t) cc_final: 0.8289 (m) REVERT: B 574 ASP cc_start: 0.8128 (t0) cc_final: 0.7791 (t0) REVERT: B 583 GLU cc_start: 0.7672 (tt0) cc_final: 0.7440 (tt0) REVERT: B 586 ASP cc_start: 0.7723 (m-30) cc_final: 0.7470 (m-30) REVERT: C 153 MET cc_start: 0.6600 (mpp) cc_final: 0.6086 (mpp) REVERT: C 169 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 281 GLU cc_start: 0.8093 (mp0) cc_final: 0.7753 (mp0) REVERT: C 309 GLU cc_start: 0.7905 (mp0) cc_final: 0.7488 (mp0) REVERT: C 567 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8073 (mtp85) REVERT: T 11 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7663 (tppp) REVERT: U 2 ASP cc_start: 0.8471 (t70) cc_final: 0.8235 (t70) REVERT: V 11 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7719 (mtpp) outliers start: 54 outliers final: 24 residues processed: 639 average time/residue: 0.5716 time to fit residues: 421.7910 Evaluate side-chains 624 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 597 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 11 LYS Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 217 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 207 HIS A 460 ASN A 501 ASN A 755 GLN A 777 ASN A 804 GLN A 969 ASN A1119 ASN B 66 HIS B 196 ASN B 271 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN B 644 GLN B1010 GLN C 30 ASN C 239 GLN C 501 ASN C1010 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.124466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107866 restraints weight = 39552.242| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.31 r_work: 0.3342 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26433 Z= 0.186 Angle : 0.632 10.435 36085 Z= 0.322 Chirality : 0.047 0.260 4205 Planarity : 0.005 0.085 4581 Dihedral : 7.059 59.657 4559 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.50 % Allowed : 12.29 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: 0.02 (0.15), residues: 3140 helix: 2.07 (0.21), residues: 676 sheet: 1.08 (0.19), residues: 693 loop : -1.35 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 995 TYR 0.024 0.001 TYR A 265 PHE 0.026 0.002 PHE C 377 TRP 0.011 0.002 TRP C 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (26333) covalent geometry : angle 0.61452 / 0.32 (35845) SS BOND : bond 0.00665 / 0.49 ( 42) SS BOND : angle 2.21240 / 1.51 ( 84) hydrogen bonds : bond 0.06355 / 4.28 ( 1023) hydrogen bonds : angle 4.99538 / 3.43 ( 2868) Misc. bond : bond 0.00084 / 0.05 ( 6) link_BETA1-4 : bond 0.00363 / 0.23 ( 15) link_BETA1-4 : angle 1.29988 / 0.82 ( 45) link_NAG-ASN : bond 0.00311 / 0.20 ( 37) link_NAG-ASN : angle 1.92704 / 1.29 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 613 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8107 (m) cc_final: 0.7699 (t) REVERT: A 374 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: A 414 GLN cc_start: 0.8596 (mm110) cc_final: 0.8277 (mp10) REVERT: A 465 GLU cc_start: 0.7702 (tp30) cc_final: 0.7403 (tp30) REVERT: A 675 GLN cc_start: 0.7928 (pp30) cc_final: 0.7567 (pp30) REVERT: A 933 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8254 (mtmt) REVERT: A 990 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7358 (mm-30) REVERT: B 147 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8113 (mtmm) REVERT: B 158 ARG cc_start: 0.8654 (mtt90) cc_final: 0.8359 (mtt90) REVERT: B 178 ASP cc_start: 0.8113 (t0) cc_final: 0.7674 (t0) REVERT: B 200 TYR cc_start: 0.8083 (m-10) cc_final: 0.7731 (m-80) REVERT: B 228 ASP cc_start: 0.6919 (t0) cc_final: 0.6686 (t0) REVERT: B 305 SER cc_start: 0.8905 (t) cc_final: 0.8697 (t) REVERT: B 364 ASP cc_start: 0.7499 (t0) cc_final: 0.7240 (t0) REVERT: B 420 ASP cc_start: 0.7897 (m-30) cc_final: 0.7645 (m-30) REVERT: B 534 VAL cc_start: 0.8560 (t) cc_final: 0.8309 (m) REVERT: B 574 ASP cc_start: 0.8153 (t0) cc_final: 0.7754 (t0) REVERT: B 583 GLU cc_start: 0.7699 (tt0) cc_final: 0.7471 (tt0) REVERT: B 811 LYS cc_start: 0.7689 (tttm) cc_final: 0.7430 (tmtm) REVERT: C 153 MET cc_start: 0.6625 (mpp) cc_final: 0.6057 (mpp) REVERT: C 169 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7271 (tm-30) REVERT: C 281 GLU cc_start: 0.8105 (mp0) cc_final: 0.7760 (mp0) REVERT: C 564 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: C 900 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8282 (mtm) REVERT: C 921 LYS cc_start: 0.8284 (mmmm) cc_final: 0.8049 (mmmm) REVERT: C 1010 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8079 (mp10) REVERT: T 11 LYS cc_start: 0.8327 (tppp) cc_final: 0.8060 (tppp) outliers start: 70 outliers final: 36 residues processed: 640 average time/residue: 0.6869 time to fit residues: 506.8609 Evaluate side-chains 643 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 604 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 196 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 207 HIS A 460 ASN A 501 ASN A 777 ASN A 969 ASN A1119 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN B1010 GLN C 30 ASN C 239 GLN C 501 ASN C 804 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107713 restraints weight = 39156.752| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.30 r_work: 0.3339 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26433 Z= 0.185 Angle : 0.636 16.335 36085 Z= 0.323 Chirality : 0.047 0.280 4205 Planarity : 0.005 0.086 4581 Dihedral : 6.834 58.580 4554 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.57 % Rotamer: Outliers : 2.68 % Allowed : 13.62 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -0.02 (0.15), residues: 3140 helix: 2.09 (0.21), residues: 676 sheet: 0.96 (0.19), residues: 698 loop : -1.36 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.024 0.001 TYR A 265 PHE 0.024 0.001 PHE C 133 TRP 0.011 0.002 TRP C 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (26333) covalent geometry : angle 0.61770 / 0.32 (35845) SS BOND : bond 0.00717 / 0.54 ( 42) SS BOND : angle 2.35131 / 1.60 ( 84) hydrogen bonds : bond 0.06356 / 4.28 ( 1023) hydrogen bonds : angle 4.96084 / 3.41 ( 2868) Misc. bond : bond 0.00052 / 0.03 ( 6) link_BETA1-4 : bond 0.00345 / 0.21 ( 15) link_BETA1-4 : angle 1.30984 / 0.82 ( 45) link_NAG-ASN : bond 0.00318 / 0.20 ( 37) link_NAG-ASN : angle 1.89859 / 1.27 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 612 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8123 (m) cc_final: 0.7698 (t) REVERT: A 374 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: A 414 GLN cc_start: 0.8599 (mm110) cc_final: 0.8252 (mp10) REVERT: A 465 GLU cc_start: 0.7681 (tp30) cc_final: 0.7378 (tp30) REVERT: A 675 GLN cc_start: 0.7942 (pp30) cc_final: 0.7682 (pp30) REVERT: A 787 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: A 990 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7335 (mm-30) REVERT: B 100 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7804 (mt) REVERT: B 147 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8073 (mtmm) REVERT: B 178 ASP cc_start: 0.8173 (t0) cc_final: 0.7724 (t0) REVERT: B 200 TYR cc_start: 0.8085 (m-10) cc_final: 0.7836 (m-80) REVERT: B 224 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 305 SER cc_start: 0.8917 (t) cc_final: 0.8715 (t) REVERT: B 364 ASP cc_start: 0.7528 (t0) cc_final: 0.7232 (t0) REVERT: B 420 ASP cc_start: 0.7912 (m-30) cc_final: 0.7682 (m-30) REVERT: B 553 THR cc_start: 0.8361 (t) cc_final: 0.8093 (p) REVERT: B 574 ASP cc_start: 0.8190 (t0) cc_final: 0.7825 (t0) REVERT: B 583 GLU cc_start: 0.7672 (tt0) cc_final: 0.7425 (tt0) REVERT: B 740 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8127 (ttp) REVERT: C 118 LEU cc_start: 0.8055 (tm) cc_final: 0.7794 (tt) REVERT: C 153 MET cc_start: 0.6638 (mpp) cc_final: 0.6002 (mpp) REVERT: C 169 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7290 (tm-30) REVERT: C 281 GLU cc_start: 0.8139 (mp0) cc_final: 0.7788 (mp0) REVERT: C 900 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8295 (mtm) REVERT: C 947 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8565 (mtpp) outliers start: 75 outliers final: 42 residues processed: 646 average time/residue: 0.6874 time to fit residues: 512.6656 Evaluate side-chains 645 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 598 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 253 optimal weight: 0.3980 chunk 117 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 228 optimal weight: 0.0570 chunk 224 optimal weight: 0.0170 chunk 80 optimal weight: 1.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 460 ASN A 501 ASN A 755 GLN A 777 ASN A 969 ASN A1119 ASN B 271 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 563 GLN B 606 ASN B 762 GLN B 913 GLN B1010 GLN C 30 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 804 GLN C1010 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.124720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.107734 restraints weight = 38934.247| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.34 r_work: 0.3373 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26433 Z= 0.116 Angle : 0.604 16.534 36085 Z= 0.305 Chirality : 0.045 0.314 4205 Planarity : 0.005 0.083 4581 Dihedral : 6.444 58.290 4553 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.89 % Rotamer: Outliers : 2.68 % Allowed : 13.97 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: 0.12 (0.15), residues: 3140 helix: 2.26 (0.21), residues: 672 sheet: 0.98 (0.18), residues: 733 loop : -1.29 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.019 0.001 TYR A 265 PHE 0.022 0.001 PHE C 133 TRP 0.010 0.001 TRP A 436 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (26333) covalent geometry : angle 0.58521 / 0.30 (35845) SS BOND : bond 0.00546 / 0.41 ( 42) SS BOND : angle 2.37798 / 1.62 ( 84) hydrogen bonds : bond 0.05345 / 3.62 ( 1023) hydrogen bonds : angle 4.82697 / 3.32 ( 2868) Misc. bond : bond 0.00020 / 0.01 ( 6) link_BETA1-4 : bond 0.00372 / 0.22 ( 15) link_BETA1-4 : angle 1.33170 / 0.83 ( 45) link_NAG-ASN : bond 0.00289 / 0.20 ( 37) link_NAG-ASN : angle 1.70383 / 1.14 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 596 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8013 (m) cc_final: 0.7596 (t) REVERT: A 374 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: A 414 GLN cc_start: 0.8573 (mm110) cc_final: 0.8266 (mp10) REVERT: A 465 GLU cc_start: 0.7637 (tp30) cc_final: 0.7319 (tp30) REVERT: A 675 GLN cc_start: 0.7916 (pp30) cc_final: 0.7601 (pp30) REVERT: A 787 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: A 933 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8098 (mtmm) REVERT: A 1072 GLU cc_start: 0.7991 (pm20) cc_final: 0.7739 (pm20) REVERT: B 97 LYS cc_start: 0.8077 (ptmm) cc_final: 0.7868 (ptmt) REVERT: B 100 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7804 (mt) REVERT: B 147 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8069 (mtmm) REVERT: B 169 GLU cc_start: 0.7983 (mp0) cc_final: 0.7754 (mp0) REVERT: B 178 ASP cc_start: 0.8130 (t0) cc_final: 0.7676 (t0) REVERT: B 224 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 305 SER cc_start: 0.8893 (t) cc_final: 0.8683 (t) REVERT: B 420 ASP cc_start: 0.7890 (m-30) cc_final: 0.7641 (m-30) REVERT: B 534 VAL cc_start: 0.8540 (t) cc_final: 0.8339 (m) REVERT: B 574 ASP cc_start: 0.8195 (t0) cc_final: 0.7796 (t0) REVERT: B 583 GLU cc_start: 0.7670 (tt0) cc_final: 0.7430 (tt0) REVERT: B 811 LYS cc_start: 0.7617 (tttm) cc_final: 0.7295 (tmtm) REVERT: B 1031 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 1096 VAL cc_start: 0.8696 (t) cc_final: 0.8464 (m) REVERT: B 1119 ASN cc_start: 0.8529 (m-40) cc_final: 0.8317 (m110) REVERT: C 118 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7873 (tt) REVERT: C 153 MET cc_start: 0.6629 (mpp) cc_final: 0.5964 (mpp) REVERT: C 169 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7234 (tm-30) REVERT: C 281 GLU cc_start: 0.8162 (mp0) cc_final: 0.7826 (mp0) REVERT: C 287 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: C 564 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: C 821 LEU cc_start: 0.8757 (tp) cc_final: 0.8542 (tt) outliers start: 75 outliers final: 35 residues processed: 627 average time/residue: 0.4544 time to fit residues: 330.8707 Evaluate side-chains 624 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 583 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 54 optimal weight: 0.8980 chunk 272 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 ASN A 501 ASN A 710 ASN A 777 ASN A 969 ASN A1119 ASN B 196 ASN B 271 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 563 GLN B 606 ASN B 914 ASN B 935 GLN B1010 GLN C 30 ASN C 239 GLN C 501 ASN C 580 GLN C 777 ASN C 804 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105082 restraints weight = 39124.009| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.35 r_work: 0.3324 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26433 Z= 0.230 Angle : 0.687 18.562 36085 Z= 0.349 Chirality : 0.049 0.374 4205 Planarity : 0.005 0.087 4581 Dihedral : 6.622 59.271 4553 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 3.25 % Allowed : 14.01 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3140 helix: 2.14 (0.21), residues: 675 sheet: 0.93 (0.18), residues: 711 loop : -1.36 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 567 TYR 0.027 0.002 TYR C 265 PHE 0.025 0.002 PHE C 133 TRP 0.013 0.002 TRP C 886 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 (26333) covalent geometry : angle 0.65953 / 0.34 (35845) SS BOND : bond 0.00744 / 0.56 ( 42) SS BOND : angle 3.36478 / 2.23 ( 84) hydrogen bonds : bond 0.06674 / 4.48 ( 1023) hydrogen bonds : angle 4.95737 / 3.40 ( 2868) Misc. bond : bond 0.00058 / 0.04 ( 6) link_BETA1-4 : bond 0.00346 / 0.20 ( 15) link_BETA1-4 : angle 1.33207 / 0.82 ( 45) link_NAG-ASN : bond 0.00393 / 0.24 ( 37) link_NAG-ASN : angle 1.94810 / 1.29 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 623 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8158 (m) cc_final: 0.7718 (t) REVERT: A 368 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 374 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: A 465 GLU cc_start: 0.7700 (tp30) cc_final: 0.7362 (tp30) REVERT: A 675 GLN cc_start: 0.7937 (pp30) cc_final: 0.7679 (pp30) REVERT: A 787 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: A 990 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 1017 GLU cc_start: 0.8090 (tp30) cc_final: 0.7826 (tp30) REVERT: A 1072 GLU cc_start: 0.8009 (pm20) cc_final: 0.7776 (pm20) REVERT: B 97 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7886 (ptmt) REVERT: B 100 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7785 (mt) REVERT: B 147 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8079 (mtmm) REVERT: B 178 ASP cc_start: 0.8106 (t0) cc_final: 0.7658 (t0) REVERT: B 200 TYR cc_start: 0.8009 (m-80) cc_final: 0.7330 (m-80) REVERT: B 224 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7404 (mt-10) REVERT: B 305 SER cc_start: 0.8923 (t) cc_final: 0.8719 (t) REVERT: B 364 ASP cc_start: 0.7507 (t0) cc_final: 0.7141 (t0) REVERT: B 420 ASP cc_start: 0.7938 (m-30) cc_final: 0.7704 (m-30) REVERT: B 534 VAL cc_start: 0.8548 (t) cc_final: 0.8303 (m) REVERT: B 574 ASP cc_start: 0.8230 (t0) cc_final: 0.7811 (t0) REVERT: B 583 GLU cc_start: 0.7722 (tt0) cc_final: 0.7470 (tt0) REVERT: B 663 ASP cc_start: 0.7972 (t0) cc_final: 0.7759 (t0) REVERT: B 811 LYS cc_start: 0.7646 (tttm) cc_final: 0.7327 (tmtm) REVERT: B 819 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7761 (mt-10) REVERT: C 118 LEU cc_start: 0.8127 (tm) cc_final: 0.7718 (tt) REVERT: C 129 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7842 (mtmm) REVERT: C 169 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7283 (tm-30) REVERT: C 281 GLU cc_start: 0.8196 (mp0) cc_final: 0.7851 (mp0) REVERT: C 428 ASP cc_start: 0.7852 (p0) cc_final: 0.7527 (p0) REVERT: C 564 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: C 614 ASP cc_start: 0.7514 (t70) cc_final: 0.7309 (t70) outliers start: 91 outliers final: 53 residues processed: 670 average time/residue: 0.6756 time to fit residues: 523.9366 Evaluate side-chains 668 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 610 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN A 207 HIS A 439 ASN A 460 ASN A 501 ASN A 506 GLN A 804 GLN A 969 ASN A1119 ASN B 196 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN B 914 ASN C 30 ASN C 501 ASN C 804 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.122471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105495 restraints weight = 38691.893| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.33 r_work: 0.3332 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26433 Z= 0.192 Angle : 0.677 18.364 36085 Z= 0.344 Chirality : 0.048 0.427 4205 Planarity : 0.005 0.090 4581 Dihedral : 6.566 58.859 4553 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.57 % Rotamer: Outliers : 3.18 % Allowed : 14.90 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3140 helix: 2.10 (0.21), residues: 675 sheet: 0.92 (0.18), residues: 712 loop : -1.36 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.025 0.001 TYR C 265 PHE 0.026 0.002 PHE C 133 TRP 0.013 0.002 TRP C 886 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (26333) covalent geometry : angle 0.65052 / 0.33 (35845) SS BOND : bond 0.00705 / 0.53 ( 42) SS BOND : angle 3.21807 / 2.12 ( 84) hydrogen bonds : bond 0.06453 / 4.34 ( 1023) hydrogen bonds : angle 4.96027 / 3.41 ( 2868) Misc. bond : bond 0.00046 / 0.03 ( 6) link_BETA1-4 : bond 0.00336 / 0.20 ( 15) link_BETA1-4 : angle 1.35549 / 0.83 ( 45) link_NAG-ASN : bond 0.00335 / 0.21 ( 37) link_NAG-ASN : angle 1.91767 / 1.28 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 608 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8145 (m) cc_final: 0.7719 (t) REVERT: A 368 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8076 (tt) REVERT: A 374 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: A 465 GLU cc_start: 0.7651 (tp30) cc_final: 0.7290 (tp30) REVERT: A 675 GLN cc_start: 0.7941 (pp30) cc_final: 0.7599 (pp30) REVERT: A 787 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: A 990 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 1017 GLU cc_start: 0.8081 (tp30) cc_final: 0.7830 (tp30) REVERT: A 1072 GLU cc_start: 0.8018 (pm20) cc_final: 0.7782 (pm20) REVERT: A 1144 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: B 97 LYS cc_start: 0.8071 (ptmm) cc_final: 0.7833 (ptmt) REVERT: B 147 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8058 (mtmm) REVERT: B 200 TYR cc_start: 0.8019 (m-80) cc_final: 0.7328 (m-80) REVERT: B 224 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 305 SER cc_start: 0.8934 (t) cc_final: 0.8725 (t) REVERT: B 364 ASP cc_start: 0.7506 (t0) cc_final: 0.7141 (t0) REVERT: B 420 ASP cc_start: 0.7946 (m-30) cc_final: 0.7700 (m-30) REVERT: B 574 ASP cc_start: 0.8226 (t0) cc_final: 0.7809 (t0) REVERT: B 583 GLU cc_start: 0.7761 (tt0) cc_final: 0.7493 (tt0) REVERT: B 664 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8207 (mt) REVERT: B 819 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 118 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7918 (tt) REVERT: C 169 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 281 GLU cc_start: 0.8180 (mp0) cc_final: 0.7825 (mp0) REVERT: C 428 ASP cc_start: 0.7849 (p0) cc_final: 0.7526 (p0) REVERT: C 564 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: C 614 ASP cc_start: 0.7499 (t70) cc_final: 0.7250 (t70) REVERT: C 821 LEU cc_start: 0.8780 (tp) cc_final: 0.8557 (tt) REVERT: C 1010 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8123 (mp10) outliers start: 89 outliers final: 53 residues processed: 652 average time/residue: 0.6725 time to fit residues: 505.3224 Evaluate side-chains 653 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 593 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 119 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 161 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 307 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 439 ASN A 460 ASN A 501 ASN A 755 GLN A 777 ASN A 804 GLN A 969 ASN A1119 ASN B 271 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN B 804 GLN B 914 ASN B1010 GLN C 30 ASN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 804 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106362 restraints weight = 39015.131| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.34 r_work: 0.3345 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26433 Z= 0.151 Angle : 0.667 18.007 36085 Z= 0.337 Chirality : 0.047 0.509 4205 Planarity : 0.005 0.088 4581 Dihedral : 6.477 58.754 4553 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 2.89 % Allowed : 15.62 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.10 % 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: 0.02 (0.15), residues: 3140 helix: 2.22 (0.21), residues: 673 sheet: 0.90 (0.18), residues: 708 loop : -1.34 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 319 TYR 0.022 0.001 TYR C 265 PHE 0.027 0.001 PHE C 133 TRP 0.012 0.001 TRP C 886 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (26333) covalent geometry : angle 0.63937 / 0.33 (35845) SS BOND : bond 0.00700 / 0.53 ( 42) SS BOND : angle 3.29760 / 2.14 ( 84) hydrogen bonds : bond 0.05993 / 4.03 ( 1023) hydrogen bonds : angle 4.90382 / 3.36 ( 2868) Misc. bond : bond 0.00031 / 0.02 ( 6) link_BETA1-4 : bond 0.00351 / 0.21 ( 15) link_BETA1-4 : angle 1.35902 / 0.84 ( 45) link_NAG-ASN : bond 0.00372 / 0.22 ( 37) link_NAG-ASN : angle 1.89063 / 1.27 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 606 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8105 (m) cc_final: 0.7686 (t) REVERT: A 368 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 374 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: A 465 GLU cc_start: 0.7644 (tp30) cc_final: 0.7285 (tp30) REVERT: A 675 GLN cc_start: 0.7930 (pp30) cc_final: 0.7667 (pp30) REVERT: A 787 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: A 1017 GLU cc_start: 0.8069 (tp30) cc_final: 0.7818 (tp30) REVERT: A 1072 GLU cc_start: 0.7991 (pm20) cc_final: 0.7755 (pm20) REVERT: B 97 LYS cc_start: 0.8077 (ptmm) cc_final: 0.7850 (ptmt) REVERT: B 147 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8046 (mtmm) REVERT: B 200 TYR cc_start: 0.8008 (m-80) cc_final: 0.7361 (m-80) REVERT: B 224 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7533 (mp0) REVERT: B 305 SER cc_start: 0.8926 (t) cc_final: 0.8716 (t) REVERT: B 364 ASP cc_start: 0.7500 (t0) cc_final: 0.7114 (t0) REVERT: B 377 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: B 420 ASP cc_start: 0.7967 (m-30) cc_final: 0.7754 (m-30) REVERT: B 574 ASP cc_start: 0.8241 (t0) cc_final: 0.7824 (t0) REVERT: B 583 GLU cc_start: 0.7741 (tt0) cc_final: 0.7472 (tt0) REVERT: B 811 LYS cc_start: 0.7692 (tttm) cc_final: 0.7406 (tmtm) REVERT: B 819 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 1119 ASN cc_start: 0.8577 (m-40) cc_final: 0.8366 (m110) REVERT: C 118 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7895 (tt) REVERT: C 169 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 281 GLU cc_start: 0.8195 (mp0) cc_final: 0.7842 (mp0) REVERT: C 428 ASP cc_start: 0.7871 (p0) cc_final: 0.7538 (p0) REVERT: C 465 GLU cc_start: 0.8136 (tp30) cc_final: 0.7851 (mp0) REVERT: C 564 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: C 614 ASP cc_start: 0.7522 (t70) cc_final: 0.7256 (t70) REVERT: C 821 LEU cc_start: 0.8775 (tp) cc_final: 0.8552 (tt) outliers start: 81 outliers final: 54 residues processed: 643 average time/residue: 0.6412 time to fit residues: 475.0710 Evaluate side-chains 654 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 594 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 196 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 108 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 0.0470 chunk 153 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 207 HIS A 460 ASN A 501 ASN A 506 GLN A 777 ASN A 804 GLN A 969 ASN A1119 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 563 GLN B 606 ASN B 914 ASN C 30 ASN C 239 GLN C 501 ASN C 804 GLN C1119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106447 restraints weight = 38948.290| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.37 r_work: 0.3346 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26433 Z= 0.152 Angle : 0.669 21.673 36085 Z= 0.337 Chirality : 0.048 0.699 4205 Planarity : 0.005 0.088 4581 Dihedral : 6.457 58.815 4553 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.57 % Rotamer: Outliers : 2.93 % Allowed : 15.69 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3140 helix: 2.25 (0.21), residues: 673 sheet: 0.85 (0.18), residues: 734 loop : -1.35 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 319 TYR 0.022 0.001 TYR C 265 PHE 0.026 0.001 PHE C 592 TRP 0.012 0.001 TRP C 886 HIS 0.016 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (26333) covalent geometry : angle 0.63987 / 0.33 (35845) SS BOND : bond 0.00801 / 0.60 ( 42) SS BOND : angle 3.27012 / 2.12 ( 84) hydrogen bonds : bond 0.05918 / 3.98 ( 1023) hydrogen bonds : angle 4.87347 / 3.35 ( 2868) Misc. bond : bond 0.00032 / 0.02 ( 6) link_BETA1-4 : bond 0.00353 / 0.21 ( 15) link_BETA1-4 : angle 1.35337 / 0.83 ( 45) link_NAG-ASN : bond 0.00370 / 0.22 ( 37) link_NAG-ASN : angle 2.08786 / 1.42 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 601 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8084 (m) cc_final: 0.7662 (t) REVERT: A 368 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8120 (tm) REVERT: A 374 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: A 465 GLU cc_start: 0.7649 (tp30) cc_final: 0.7282 (tp30) REVERT: A 675 GLN cc_start: 0.7936 (pp30) cc_final: 0.7597 (pp30) REVERT: A 787 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: A 1017 GLU cc_start: 0.8079 (tp30) cc_final: 0.7822 (tp30) REVERT: A 1072 GLU cc_start: 0.7992 (pm20) cc_final: 0.7750 (pm20) REVERT: B 97 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7849 (ptmt) REVERT: B 147 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8060 (mtmm) REVERT: B 200 TYR cc_start: 0.8004 (m-80) cc_final: 0.7337 (m-80) REVERT: B 224 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 305 SER cc_start: 0.8942 (t) cc_final: 0.8731 (t) REVERT: B 364 ASP cc_start: 0.7496 (t0) cc_final: 0.7113 (t0) REVERT: B 377 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: B 420 ASP cc_start: 0.7960 (m-30) cc_final: 0.7748 (m-30) REVERT: B 574 ASP cc_start: 0.8244 (t0) cc_final: 0.7833 (t0) REVERT: B 583 GLU cc_start: 0.7750 (tt0) cc_final: 0.7483 (tt0) REVERT: B 664 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8193 (mt) REVERT: B 819 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 914 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7465 (p0) REVERT: C 118 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7889 (tt) REVERT: C 169 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 239 GLN cc_start: 0.8156 (tt0) cc_final: 0.7951 (tt0) REVERT: C 281 GLU cc_start: 0.8182 (mp0) cc_final: 0.7825 (mp0) REVERT: C 428 ASP cc_start: 0.7866 (p0) cc_final: 0.7537 (p0) REVERT: C 465 GLU cc_start: 0.8147 (tp30) cc_final: 0.7878 (mp0) REVERT: C 564 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: C 614 ASP cc_start: 0.7544 (t70) cc_final: 0.7275 (t70) REVERT: C 821 LEU cc_start: 0.8772 (tp) cc_final: 0.8548 (tt) REVERT: C 934 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7928 (mt) outliers start: 82 outliers final: 60 residues processed: 639 average time/residue: 0.6731 time to fit residues: 495.4687 Evaluate side-chains 664 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 595 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 285 optimal weight: 0.0670 chunk 118 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 267 optimal weight: 0.5980 chunk 283 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 460 ASN A 501 ASN A 556 ASN A 777 ASN A 969 ASN A1119 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 564 GLN B 606 ASN B 914 ASN B1010 GLN B1119 ASN C 30 ASN C 501 ASN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106565 restraints weight = 38933.145| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.34 r_work: 0.3348 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26433 Z= 0.156 Angle : 0.678 21.848 36085 Z= 0.342 Chirality : 0.048 0.625 4205 Planarity : 0.005 0.093 4581 Dihedral : 6.429 58.765 4553 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 2.72 % Allowed : 16.12 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3140 helix: 2.23 (0.21), residues: 673 sheet: 0.90 (0.18), residues: 718 loop : -1.34 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 319 TYR 0.022 0.001 TYR C 265 PHE 0.030 0.001 PHE C 592 TRP 0.012 0.001 TRP C 886 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (26333) covalent geometry : angle 0.65009 / 0.33 (35845) SS BOND : bond 0.00756 / 0.57 ( 42) SS BOND : angle 3.30526 / 2.13 ( 84) hydrogen bonds : bond 0.05924 / 3.98 ( 1023) hydrogen bonds : angle 4.86932 / 3.35 ( 2868) Misc. bond : bond 0.00034 / 0.02 ( 6) link_BETA1-4 : bond 0.00349 / 0.21 ( 15) link_BETA1-4 : angle 1.35096 / 0.83 ( 45) link_NAG-ASN : bond 0.00356 / 0.21 ( 37) link_NAG-ASN : angle 2.01759 / 1.37 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 596 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8078 (m) cc_final: 0.7666 (t) REVERT: A 368 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 374 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: A 465 GLU cc_start: 0.7653 (tp30) cc_final: 0.7277 (tp30) REVERT: A 675 GLN cc_start: 0.7931 (pp30) cc_final: 0.7665 (pp30) REVERT: A 787 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: A 1017 GLU cc_start: 0.8079 (tp30) cc_final: 0.7816 (tp30) REVERT: A 1072 GLU cc_start: 0.7981 (pm20) cc_final: 0.7739 (pm20) REVERT: B 100 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 147 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8051 (mtmm) REVERT: B 200 TYR cc_start: 0.8010 (m-80) cc_final: 0.7356 (m-80) REVERT: B 305 SER cc_start: 0.8922 (t) cc_final: 0.8700 (t) REVERT: B 364 ASP cc_start: 0.7501 (t0) cc_final: 0.7111 (t0) REVERT: B 377 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: B 420 ASP cc_start: 0.7971 (m-30) cc_final: 0.7760 (m-30) REVERT: B 574 ASP cc_start: 0.8255 (t0) cc_final: 0.7850 (t0) REVERT: B 583 GLU cc_start: 0.7744 (tt0) cc_final: 0.7475 (tt0) REVERT: B 664 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8195 (mt) REVERT: C 118 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7882 (tt) REVERT: C 169 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 281 GLU cc_start: 0.8187 (mp0) cc_final: 0.7829 (mp0) REVERT: C 428 ASP cc_start: 0.7869 (p0) cc_final: 0.7544 (p0) REVERT: C 465 GLU cc_start: 0.8140 (tp30) cc_final: 0.7871 (mp0) REVERT: C 564 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: C 614 ASP cc_start: 0.7549 (t70) cc_final: 0.7257 (t70) REVERT: C 821 LEU cc_start: 0.8770 (tp) cc_final: 0.8549 (tt) REVERT: C 934 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7921 (mt) outliers start: 76 outliers final: 62 residues processed: 630 average time/residue: 0.6668 time to fit residues: 484.8663 Evaluate side-chains 660 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 589 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain V residue 11 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 116 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 162 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 460 ASN A 501 ASN A 777 ASN A 969 ASN A1119 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN B1010 GLN C 30 ASN C 239 GLN C 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106498 restraints weight = 38804.496| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.34 r_work: 0.3345 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26433 Z= 0.164 Angle : 0.686 21.205 36085 Z= 0.345 Chirality : 0.048 0.715 4205 Planarity : 0.005 0.092 4581 Dihedral : 6.438 58.761 4553 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 2.82 % Allowed : 16.30 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3140 helix: 2.23 (0.21), residues: 673 sheet: 0.90 (0.18), residues: 718 loop : -1.35 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 319 TYR 0.023 0.001 TYR C 265 PHE 0.030 0.001 PHE C 592 TRP 0.013 0.001 TRP C 886 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (26333) covalent geometry : angle 0.65349 / 0.33 (35845) SS BOND : bond 0.00742 / 0.56 ( 42) SS BOND : angle 3.25481 / 2.09 ( 84) hydrogen bonds : bond 0.06008 / 4.03 ( 1023) hydrogen bonds : angle 4.87351 / 3.35 ( 2868) Misc. bond : bond 0.00034 / 0.02 ( 6) link_BETA1-4 : bond 0.00355 / 0.21 ( 15) link_BETA1-4 : angle 1.35090 / 0.83 ( 45) link_NAG-ASN : bond 0.00315 / 0.20 ( 37) link_NAG-ASN : angle 2.51025 / 1.73 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11992.06 seconds wall clock time: 215 minutes 45.55 seconds (12945.55 seconds total)