Starting phenix.real_space_refine on Tue Apr 7 08:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3q_62788/04_2026/9l3q_62788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3q_62788/04_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_62788/04_2026/9l3q_62788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3q_62788/04_2026/9l3q_62788.map" model { file = "/net/cci-nas-00/data/ceres_data/9l3q_62788/04_2026/9l3q_62788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3q_62788/04_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-2.1rc1-6017/lib/python3.9/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 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 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 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: 5.44, per 1000 atoms: 0.21 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: 2.27 Conformation dependent library (CDL) restraints added in 1.0 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: 1.20 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: 5.86 Time building geometry restraints manager: 2.98 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: 34594 1.77 - 3.54: 1078 3.54 - 5.31: 147 5.31 - 7.08: 21 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: 14991 19.72 - 39.44: 1138 39.44 - 59.16: 174 59.16 - 78.87: 50 78.87 - 98.59: 16 Dihedral angle restraints: 16369 sinusoidal: 7067 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 16366 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: 10.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.810 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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= 0.266 Angle : 0.721 8.855 36085 Z= 0.396 Chirality : 0.048 0.304 4205 Planarity : 0.005 0.089 4581 Dihedral : 13.776 98.593 10261 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 covalent geometry : bond 0.00419 (26333) covalent geometry : angle 0.69966 (35845) SS BOND : bond 0.00457 ( 42) SS BOND : angle 2.46105 ( 84) hydrogen bonds : bond 0.12818 ( 1023) hydrogen bonds : angle 5.97511 ( 2868) Misc. bond : bond 0.10170 ( 6) link_BETA1-4 : bond 0.00431 ( 15) link_BETA1-4 : angle 1.47850 ( 45) link_NAG-ASN : bond 0.00357 ( 37) link_NAG-ASN : angle 2.35202 ( 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 : 0.707 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: 0.6805 time to fit residues: 492.0756 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 : 0.931 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.125540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108953 restraints weight = 39421.078| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.31 r_work: 0.3359 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26433 Z= 0.176 Angle : 0.647 9.391 36085 Z= 0.327 Chirality : 0.047 0.300 4205 Planarity : 0.005 0.072 4581 Dihedral : 7.418 61.764 4543 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.24 % Favored : 95.57 % Rotamer: Outliers : 1.86 % Allowed : 10.04 % Favored : 88.10 % Cbeta Deviations : 0.10 % 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: 0.05 (0.15), residues: 3140 helix: 2.07 (0.21), residues: 676 sheet: 1.24 (0.18), residues: 696 loop : -1.39 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 995 TYR 0.022 0.002 TYR A 265 PHE 0.017 0.001 PHE A 347 TRP 0.010 0.001 TRP A 436 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00423 (26333) covalent geometry : angle 0.62855 (35845) SS BOND : bond 0.00535 ( 42) SS BOND : angle 2.05891 ( 84) hydrogen bonds : bond 0.06245 ( 1023) hydrogen bonds : angle 5.09476 ( 2868) Misc. bond : bond 0.00219 ( 6) link_BETA1-4 : bond 0.00411 ( 15) link_BETA1-4 : angle 1.29401 ( 45) link_NAG-ASN : bond 0.00326 ( 37) link_NAG-ASN : angle 2.10870 ( 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 673 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 621 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.7990 (m) cc_final: 0.7585 (t) REVERT: A 408 ARG cc_start: 0.8669 (ptm-80) cc_final: 0.8134 (ptm-80) REVERT: A 414 GLN cc_start: 0.8573 (mm110) cc_final: 0.8334 (mp10) REVERT: A 465 GLU cc_start: 0.7693 (tp30) cc_final: 0.7421 (tp30) REVERT: A 675 GLN cc_start: 0.7892 (pp30) cc_final: 0.7463 (pp30) REVERT: A 912 THR cc_start: 0.8457 (m) cc_final: 0.8210 (p) REVERT: A 1017 GLU cc_start: 0.7821 (tp30) cc_final: 0.7363 (tp30) REVERT: B 97 LYS cc_start: 0.8194 (ptpp) cc_final: 0.7888 (ptpp) REVERT: B 178 ASP cc_start: 0.8138 (t0) cc_final: 0.7709 (t0) REVERT: B 200 TYR cc_start: 0.8024 (m-10) cc_final: 0.7712 (m-80) REVERT: B 228 ASP cc_start: 0.6973 (t0) cc_final: 0.6467 (t70) REVERT: B 354 ASN cc_start: 0.8160 (t0) cc_final: 0.7893 (t0) REVERT: B 364 ASP cc_start: 0.7465 (t0) cc_final: 0.7244 (t0) REVERT: B 420 ASP cc_start: 0.7842 (m-30) cc_final: 0.7599 (m-30) REVERT: B 534 VAL cc_start: 0.8553 (t) cc_final: 0.8288 (m) REVERT: B 574 ASP cc_start: 0.8130 (t0) cc_final: 0.7791 (t0) REVERT: B 583 GLU cc_start: 0.7671 (tt0) cc_final: 0.7435 (tt0) REVERT: B 586 ASP cc_start: 0.7714 (m-30) cc_final: 0.7466 (m-30) REVERT: B 823 PHE cc_start: 0.7784 (m-80) cc_final: 0.7582 (m-80) REVERT: C 153 MET cc_start: 0.6615 (mpp) cc_final: 0.6085 (mpp) REVERT: C 169 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 281 GLU cc_start: 0.8092 (mp0) cc_final: 0.7753 (mp0) REVERT: C 309 GLU cc_start: 0.7904 (mp0) cc_final: 0.7482 (mp0) REVERT: C 567 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8066 (mtp85) REVERT: T 11 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7674 (tppp) REVERT: V 11 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7737 (mtpp) outliers start: 52 outliers final: 23 residues processed: 639 average time/residue: 0.6694 time to fit residues: 490.3460 Evaluate side-chains 623 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 597 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 287 ASP 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 T residue 6 THR Chi-restraints excluded: chain T residue 11 LYS 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: 0.8980 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107740 restraints weight = 39579.045| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.32 r_work: 0.3339 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26433 Z= 0.192 Angle : 0.640 9.931 36085 Z= 0.325 Chirality : 0.047 0.262 4205 Planarity : 0.005 0.086 4581 Dihedral : 6.957 59.207 4535 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 2.39 % Allowed : 12.26 % Favored : 85.35 % Cbeta Deviations : 0.03 % 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: 0.00 (0.15), residues: 3140 helix: 2.07 (0.21), residues: 676 sheet: 1.04 (0.19), residues: 684 loop : -1.34 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 995 TYR 0.024 0.002 TYR C 265 PHE 0.026 0.002 PHE C 377 TRP 0.011 0.002 TRP C 436 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00467 (26333) covalent geometry : angle 0.62159 (35845) SS BOND : bond 0.00814 ( 42) SS BOND : angle 2.30740 ( 84) hydrogen bonds : bond 0.06437 ( 1023) hydrogen bonds : angle 5.00677 ( 2868) Misc. bond : bond 0.00043 ( 6) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.29384 ( 45) link_NAG-ASN : bond 0.00296 ( 37) link_NAG-ASN : angle 1.95139 ( 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: 67 poor density : 616 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8115 (m) cc_final: 0.7709 (t) REVERT: A 374 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: A 408 ARG cc_start: 0.8668 (ptm-80) cc_final: 0.8385 (ptm-80) REVERT: A 414 GLN cc_start: 0.8590 (mm110) cc_final: 0.8274 (mp10) REVERT: A 465 GLU cc_start: 0.7686 (tp30) cc_final: 0.7388 (tp30) REVERT: A 675 GLN cc_start: 0.7932 (pp30) cc_final: 0.7678 (pp30) REVERT: A 787 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: A 990 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 147 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8116 (mtmm) REVERT: B 158 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8390 (mtt90) REVERT: B 178 ASP cc_start: 0.8119 (t0) cc_final: 0.7679 (t0) REVERT: B 200 TYR cc_start: 0.8087 (m-10) cc_final: 0.7733 (m-80) REVERT: B 228 ASP cc_start: 0.6921 (t0) cc_final: 0.6681 (t0) REVERT: B 305 SER cc_start: 0.8904 (t) cc_final: 0.8694 (t) REVERT: B 364 ASP cc_start: 0.7503 (t0) cc_final: 0.7270 (t0) REVERT: B 420 ASP cc_start: 0.7897 (m-30) cc_final: 0.7648 (m-30) REVERT: B 534 VAL cc_start: 0.8559 (t) cc_final: 0.8308 (m) REVERT: B 574 ASP cc_start: 0.8159 (t0) cc_final: 0.7760 (t0) REVERT: B 583 GLU cc_start: 0.7709 (tt0) cc_final: 0.7484 (tt0) REVERT: B 586 ASP cc_start: 0.7734 (m-30) cc_final: 0.7534 (m-30) REVERT: B 811 LYS cc_start: 0.7693 (tttm) cc_final: 0.7435 (tmtm) REVERT: B 823 PHE cc_start: 0.7892 (m-80) cc_final: 0.7666 (m-80) REVERT: C 153 MET cc_start: 0.6619 (mpp) cc_final: 0.6046 (mpp) REVERT: C 169 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 281 GLU cc_start: 0.8122 (mp0) cc_final: 0.7778 (mp0) REVERT: C 564 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: C 900 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: C 921 LYS cc_start: 0.8284 (mmmm) cc_final: 0.8050 (mmmm) REVERT: C 1010 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8074 (mp10) REVERT: T 11 LYS cc_start: 0.8329 (tppp) cc_final: 0.7631 (tppp) outliers start: 67 outliers final: 37 residues processed: 641 average time/residue: 0.6824 time to fit residues: 501.1465 Evaluate side-chains 644 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 603 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 138 ASP 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 754 LEU Chi-restraints excluded: chain A residue 787 GLN 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 120 VAL 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 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: 0.6980 chunk 149 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 260 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 460 ASN A 501 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 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN B 913 GLN B1010 GLN C 30 ASN C 239 GLN C 501 ASN C 804 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.124314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107782 restraints weight = 39158.245| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.30 r_work: 0.3341 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26433 Z= 0.175 Angle : 0.632 15.572 36085 Z= 0.320 Chirality : 0.047 0.271 4205 Planarity : 0.005 0.086 4581 Dihedral : 6.660 58.559 4530 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 2.82 % Allowed : 13.58 % Favored : 83.60 % 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: -0.01 (0.15), residues: 3140 helix: 2.10 (0.21), residues: 675 sheet: 0.99 (0.19), residues: 697 loop : -1.35 (0.13), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.024 0.001 TYR C 265 PHE 0.025 0.001 PHE C 133 TRP 0.011 0.001 TRP C 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00422 (26333) covalent geometry : angle 0.61410 (35845) SS BOND : bond 0.00754 ( 42) SS BOND : angle 2.27567 ( 84) hydrogen bonds : bond 0.06257 ( 1023) hydrogen bonds : angle 4.94260 ( 2868) Misc. bond : bond 0.00057 ( 6) link_BETA1-4 : bond 0.00362 ( 15) link_BETA1-4 : angle 1.30911 ( 45) link_NAG-ASN : bond 0.00323 ( 37) link_NAG-ASN : angle 1.86796 ( 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 691 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 612 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8132 (m) cc_final: 0.7696 (t) REVERT: A 374 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: A 408 ARG cc_start: 0.8675 (ptm-80) cc_final: 0.8423 (ptm-80) REVERT: A 414 GLN cc_start: 0.8600 (mm110) cc_final: 0.8262 (mp10) REVERT: A 465 GLU cc_start: 0.7680 (tp30) cc_final: 0.7372 (tp30) REVERT: A 675 GLN cc_start: 0.7933 (pp30) cc_final: 0.7679 (pp30) REVERT: A 787 GLN cc_start: 0.8351 (mt0) cc_final: 0.8072 (mt0) REVERT: B 100 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7788 (mt) REVERT: B 147 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8071 (mtmm) REVERT: B 178 ASP cc_start: 0.8174 (t0) cc_final: 0.7721 (t0) REVERT: B 200 TYR cc_start: 0.8079 (m-10) cc_final: 0.7836 (m-80) REVERT: B 305 SER cc_start: 0.8913 (t) cc_final: 0.8707 (t) REVERT: B 364 ASP cc_start: 0.7533 (t0) cc_final: 0.7250 (t0) REVERT: B 420 ASP cc_start: 0.7918 (m-30) cc_final: 0.7688 (m-30) REVERT: B 534 VAL cc_start: 0.8553 (t) cc_final: 0.8302 (m) REVERT: B 553 THR cc_start: 0.8384 (t) cc_final: 0.8108 (p) REVERT: B 574 ASP cc_start: 0.8178 (t0) cc_final: 0.7755 (t0) REVERT: B 583 GLU cc_start: 0.7698 (tt0) cc_final: 0.7433 (tt0) REVERT: B 586 ASP cc_start: 0.7740 (m-30) cc_final: 0.7514 (m-30) REVERT: B 819 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7559 (mt-10) REVERT: C 118 LEU cc_start: 0.8106 (tm) cc_final: 0.7829 (tt) REVERT: C 153 MET cc_start: 0.6637 (mpp) cc_final: 0.6000 (mpp) REVERT: C 169 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 281 GLU cc_start: 0.8135 (mp0) cc_final: 0.7782 (mp0) REVERT: C 821 LEU cc_start: 0.8774 (tp) cc_final: 0.8550 (tt) REVERT: C 900 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: C 947 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8579 (mtpp) REVERT: T 11 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7618 (tppp) outliers start: 79 outliers final: 40 residues processed: 649 average time/residue: 0.6897 time to fit residues: 512.9408 Evaluate side-chains 635 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 591 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 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 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 335 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 GLU 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 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 T residue 11 LYS 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: 1.9990 chunk 117 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 257 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 293 optimal weight: 0.5980 chunk 228 optimal weight: 0.0270 chunk 224 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 580 GLN C 804 GLN C1010 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106376 restraints weight = 38891.663| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.34 r_work: 0.3350 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26433 Z= 0.151 Angle : 0.629 17.994 36085 Z= 0.318 Chirality : 0.046 0.331 4205 Planarity : 0.005 0.085 4581 Dihedral : 6.466 58.628 4529 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.79 % Allowed : 14.08 % Favored : 83.13 % 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: 2.14 (0.21), residues: 675 sheet: 0.97 (0.18), residues: 716 loop : -1.35 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.022 0.001 TYR C 265 PHE 0.024 0.001 PHE C 133 TRP 0.011 0.001 TRP A 436 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00357 (26333) covalent geometry : angle 0.60800 (35845) SS BOND : bond 0.00625 ( 42) SS BOND : angle 2.61998 ( 84) hydrogen bonds : bond 0.05963 ( 1023) hydrogen bonds : angle 4.89576 ( 2868) Misc. bond : bond 0.00039 ( 6) link_BETA1-4 : bond 0.00358 ( 15) link_BETA1-4 : angle 1.32397 ( 45) link_NAG-ASN : bond 0.00346 ( 37) link_NAG-ASN : angle 1.80590 ( 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 672 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 594 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8095 (m) cc_final: 0.7673 (t) REVERT: A 374 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: A 408 ARG cc_start: 0.8656 (ptm-80) cc_final: 0.8415 (ptm-80) REVERT: A 414 GLN cc_start: 0.8594 (mm110) cc_final: 0.8299 (mp10) REVERT: A 465 GLU cc_start: 0.7660 (tp30) cc_final: 0.7337 (tp30) REVERT: A 675 GLN cc_start: 0.7925 (pp30) cc_final: 0.7562 (pp30) REVERT: A 787 GLN cc_start: 0.8386 (mt0) cc_final: 0.8101 (mt0) REVERT: B 97 LYS cc_start: 0.8061 (ptmm) cc_final: 0.7843 (ptmt) REVERT: B 100 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7798 (mt) REVERT: B 147 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8081 (mtmm) REVERT: B 178 ASP cc_start: 0.8074 (t0) cc_final: 0.7628 (t0) REVERT: B 200 TYR cc_start: 0.8067 (m-10) cc_final: 0.7831 (m-80) REVERT: B 305 SER cc_start: 0.8892 (t) cc_final: 0.8677 (t) REVERT: B 364 ASP cc_start: 0.7547 (t0) cc_final: 0.7245 (t0) REVERT: B 420 ASP cc_start: 0.7924 (m-30) cc_final: 0.7680 (m-30) REVERT: B 553 THR cc_start: 0.8392 (t) cc_final: 0.8119 (p) REVERT: B 574 ASP cc_start: 0.8192 (t0) cc_final: 0.7768 (t0) REVERT: B 583 GLU cc_start: 0.7729 (tt0) cc_final: 0.7484 (tt0) REVERT: B 586 ASP cc_start: 0.7743 (m-30) cc_final: 0.7521 (m-30) REVERT: B 811 LYS cc_start: 0.7641 (tttm) cc_final: 0.7322 (tmtm) REVERT: B 1096 VAL cc_start: 0.8711 (t) cc_final: 0.8491 (m) REVERT: C 118 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7894 (tt) REVERT: C 169 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 281 GLU cc_start: 0.8175 (mp0) cc_final: 0.7828 (mp0) REVERT: C 564 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: C 900 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8278 (mtm) REVERT: T 11 LYS cc_start: 0.8313 (tppp) cc_final: 0.7656 (tppp) outliers start: 78 outliers final: 52 residues processed: 629 average time/residue: 0.6717 time to fit residues: 486.0785 Evaluate side-chains 633 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 576 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 207 HIS 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 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 826 VAL 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 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 393 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL 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 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 914 ASN 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 B residue 1100 THR 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 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 773 GLU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 914 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 54 optimal weight: 4.9990 chunk 272 optimal weight: 0.0770 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 251 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107032 restraints weight = 39144.416| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.35 r_work: 0.3356 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26433 Z= 0.134 Angle : 0.619 14.577 36085 Z= 0.312 Chirality : 0.046 0.341 4205 Planarity : 0.005 0.084 4581 Dihedral : 6.294 58.664 4529 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.80 % Rotamer: Outliers : 2.97 % Allowed : 14.30 % Favored : 82.74 % 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: 0.07 (0.15), residues: 3140 helix: 2.23 (0.21), residues: 672 sheet: 0.94 (0.18), residues: 720 loop : -1.31 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.021 0.001 TYR A 265 PHE 0.025 0.001 PHE C 133 TRP 0.010 0.001 TRP C 436 HIS 0.015 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00311 (26333) covalent geometry : angle 0.59699 (35845) SS BOND : bond 0.00610 ( 42) SS BOND : angle 2.69453 ( 84) hydrogen bonds : bond 0.05670 ( 1023) hydrogen bonds : angle 4.85592 ( 2868) Misc. bond : bond 0.00029 ( 6) link_BETA1-4 : bond 0.00359 ( 15) link_BETA1-4 : angle 1.32596 ( 45) link_NAG-ASN : bond 0.00278 ( 37) link_NAG-ASN : angle 1.76142 ( 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 673 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 590 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8064 (m) cc_final: 0.7646 (t) REVERT: A 368 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 374 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: A 376 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7836 (p) REVERT: A 408 ARG cc_start: 0.8655 (ptm-80) cc_final: 0.8441 (ptm-80) REVERT: A 414 GLN cc_start: 0.8587 (mm110) cc_final: 0.8269 (mp10) REVERT: A 465 GLU cc_start: 0.7686 (tp30) cc_final: 0.7347 (tp30) REVERT: A 675 GLN cc_start: 0.7918 (pp30) cc_final: 0.7576 (pp30) REVERT: A 787 GLN cc_start: 0.8389 (mt0) cc_final: 0.8103 (mt0) REVERT: A 1017 GLU cc_start: 0.8075 (tp30) cc_final: 0.7850 (tp30) REVERT: A 1072 GLU cc_start: 0.7954 (pm20) cc_final: 0.7694 (pm20) REVERT: B 100 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7786 (mt) REVERT: B 147 LYS cc_start: 0.8364 (mtmm) cc_final: 0.8080 (mtmm) REVERT: B 158 ARG cc_start: 0.8538 (mtt90) cc_final: 0.7922 (mtt-85) REVERT: B 178 ASP cc_start: 0.8091 (t0) cc_final: 0.7650 (t0) REVERT: B 200 TYR cc_start: 0.8049 (m-10) cc_final: 0.7823 (m-80) REVERT: B 305 SER cc_start: 0.8899 (t) cc_final: 0.8682 (t) REVERT: B 420 ASP cc_start: 0.7925 (m-30) cc_final: 0.7696 (m-30) REVERT: B 534 VAL cc_start: 0.8556 (t) cc_final: 0.8334 (m) REVERT: B 553 THR cc_start: 0.8394 (t) cc_final: 0.8131 (p) REVERT: B 574 ASP cc_start: 0.8219 (t0) cc_final: 0.7790 (t0) REVERT: B 583 GLU cc_start: 0.7741 (tt0) cc_final: 0.7489 (tt0) REVERT: B 811 LYS cc_start: 0.7646 (tttm) cc_final: 0.7377 (tmtm) REVERT: B 1096 VAL cc_start: 0.8718 (t) cc_final: 0.8506 (m) REVERT: B 1119 ASN cc_start: 0.8548 (m-40) cc_final: 0.8343 (m110) REVERT: C 169 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7257 (tm-30) REVERT: C 281 GLU cc_start: 0.8181 (mp0) cc_final: 0.7841 (mp0) REVERT: C 428 ASP cc_start: 0.7822 (p0) cc_final: 0.7502 (p0) REVERT: C 821 LEU cc_start: 0.8759 (tp) cc_final: 0.8545 (tt) REVERT: C 900 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8283 (mtm) REVERT: T 11 LYS cc_start: 0.8328 (tppp) cc_final: 0.7680 (tppp) outliers start: 83 outliers final: 47 residues processed: 631 average time/residue: 0.6583 time to fit residues: 479.0983 Evaluate side-chains 635 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 583 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 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 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 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 171 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 472 ILE 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 705 VAL Chi-restraints excluded: chain B residue 878 LEU 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 B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL 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 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 900 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 76 optimal weight: 0.0270 chunk 204 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN 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 540 ASN B 563 GLN B 606 ASN B 914 ASN C 30 ASN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 777 ASN C 804 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106965 restraints weight = 38712.717| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.34 r_work: 0.3357 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26433 Z= 0.143 Angle : 0.643 19.717 36085 Z= 0.324 Chirality : 0.047 0.434 4205 Planarity : 0.005 0.084 4581 Dihedral : 6.239 58.780 4529 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 3.22 % Allowed : 14.62 % Favored : 82.17 % 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: 0.09 (0.15), residues: 3140 helix: 2.25 (0.21), residues: 673 sheet: 0.98 (0.18), residues: 712 loop : -1.30 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 567 TYR 0.021 0.001 TYR C 265 PHE 0.028 0.001 PHE C 133 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00338 (26333) covalent geometry : angle 0.61818 (35845) SS BOND : bond 0.00651 ( 42) SS BOND : angle 3.08144 ( 84) hydrogen bonds : bond 0.05695 ( 1023) hydrogen bonds : angle 4.84477 ( 2868) Misc. bond : bond 0.00031 ( 6) link_BETA1-4 : bond 0.00353 ( 15) link_BETA1-4 : angle 1.32109 ( 45) link_NAG-ASN : bond 0.00350 ( 37) link_NAG-ASN : angle 1.79363 ( 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 683 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 593 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8070 (m) cc_final: 0.7626 (t) REVERT: A 368 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8126 (tt) REVERT: A 374 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: A 376 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7847 (p) REVERT: A 408 ARG cc_start: 0.8656 (ptm-80) cc_final: 0.8436 (ptm-80) REVERT: A 414 GLN cc_start: 0.8585 (mm110) cc_final: 0.8271 (mp10) REVERT: A 465 GLU cc_start: 0.7665 (tp30) cc_final: 0.7337 (tp30) REVERT: A 675 GLN cc_start: 0.7918 (pp30) cc_final: 0.7583 (pp30) REVERT: A 787 GLN cc_start: 0.8385 (mt0) cc_final: 0.8095 (mt0) REVERT: A 1017 GLU cc_start: 0.8077 (tp30) cc_final: 0.7850 (tp30) REVERT: A 1072 GLU cc_start: 0.7952 (pm20) cc_final: 0.7688 (pm20) REVERT: B 100 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7739 (mt) REVERT: B 147 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8052 (mtmm) REVERT: B 178 ASP cc_start: 0.8119 (t0) cc_final: 0.7665 (t0) REVERT: B 200 TYR cc_start: 0.8050 (m-10) cc_final: 0.7733 (m-80) REVERT: B 305 SER cc_start: 0.8907 (t) cc_final: 0.8695 (t) REVERT: B 420 ASP cc_start: 0.7920 (m-30) cc_final: 0.7699 (m-30) REVERT: B 534 VAL cc_start: 0.8536 (t) cc_final: 0.8311 (m) REVERT: B 554 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 574 ASP cc_start: 0.8226 (t0) cc_final: 0.7800 (t0) REVERT: B 583 GLU cc_start: 0.7761 (tt0) cc_final: 0.7496 (tt0) REVERT: B 586 ASP cc_start: 0.7828 (m-30) cc_final: 0.7611 (m-30) REVERT: B 663 ASP cc_start: 0.7956 (t0) cc_final: 0.7730 (t0) REVERT: B 914 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 1119 ASN cc_start: 0.8548 (m-40) cc_final: 0.8345 (m110) REVERT: C 169 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C 281 GLU cc_start: 0.8182 (mp0) cc_final: 0.7832 (mp0) REVERT: C 428 ASP cc_start: 0.7837 (p0) cc_final: 0.7505 (p0) REVERT: C 564 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: C 614 ASP cc_start: 0.7485 (t70) cc_final: 0.7252 (t70) REVERT: C 821 LEU cc_start: 0.8764 (tp) cc_final: 0.8545 (tt) REVERT: C 900 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8283 (mtm) REVERT: T 11 LYS cc_start: 0.8312 (tppp) cc_final: 0.7662 (tppp) outliers start: 90 outliers final: 52 residues processed: 635 average time/residue: 0.6354 time to fit residues: 464.4094 Evaluate side-chains 645 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 586 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 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 433 VAL 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 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 120 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 360 ASN 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 697 MET Chi-restraints excluded: chain B residue 705 VAL 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 1073 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 385 THR 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 754 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 900 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 119 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.0060 chunk 296 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 172 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 914 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.123174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106158 restraints weight = 38936.446| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.35 r_work: 0.3343 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26433 Z= 0.177 Angle : 0.664 18.107 36085 Z= 0.336 Chirality : 0.048 0.523 4205 Planarity : 0.005 0.085 4581 Dihedral : 6.284 58.917 4529 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 3.15 % Allowed : 15.15 % Favored : 81.70 % 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: 2.20 (0.21), residues: 673 sheet: 0.92 (0.18), residues: 708 loop : -1.33 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 567 TYR 0.024 0.001 TYR A 265 PHE 0.028 0.001 PHE C 133 TRP 0.013 0.001 TRP C 886 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00427 (26333) covalent geometry : angle 0.63799 (35845) SS BOND : bond 0.00721 ( 42) SS BOND : angle 3.19828 ( 84) hydrogen bonds : bond 0.06116 ( 1023) hydrogen bonds : angle 4.89162 ( 2868) Misc. bond : bond 0.00045 ( 6) link_BETA1-4 : bond 0.00344 ( 15) link_BETA1-4 : angle 1.32814 ( 45) link_NAG-ASN : bond 0.00339 ( 37) link_NAG-ASN : angle 1.90029 ( 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 683 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 595 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8118 (m) cc_final: 0.7690 (t) REVERT: A 368 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8141 (tm) REVERT: A 374 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: A 414 GLN cc_start: 0.8594 (mm110) cc_final: 0.8388 (mp10) REVERT: A 465 GLU cc_start: 0.7653 (tp30) cc_final: 0.7294 (tp30) REVERT: A 675 GLN cc_start: 0.7914 (pp30) cc_final: 0.7658 (pp30) REVERT: A 787 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: A 1017 GLU cc_start: 0.8065 (tp30) cc_final: 0.7815 (tp30) REVERT: A 1072 GLU cc_start: 0.7977 (pm20) cc_final: 0.7739 (pm20) REVERT: B 97 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7873 (ptmt) REVERT: B 147 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8082 (mtmm) REVERT: B 200 TYR cc_start: 0.8016 (m-10) cc_final: 0.7776 (m-80) REVERT: B 364 ASP cc_start: 0.7509 (t0) cc_final: 0.7140 (t0) REVERT: B 377 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: B 420 ASP cc_start: 0.7935 (m-30) cc_final: 0.7693 (m-30) REVERT: B 574 ASP cc_start: 0.8228 (t0) cc_final: 0.7802 (t0) REVERT: B 583 GLU cc_start: 0.7772 (tt0) cc_final: 0.7502 (tt0) REVERT: B 586 ASP cc_start: 0.7825 (m-30) cc_final: 0.7605 (m-30) REVERT: B 663 ASP cc_start: 0.7962 (t0) cc_final: 0.7720 (t0) REVERT: B 664 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8133 (mt) REVERT: B 811 LYS cc_start: 0.7650 (tmtm) cc_final: 0.7313 (tmtm) REVERT: B 994 ASP cc_start: 0.7653 (m-30) cc_final: 0.7449 (m-30) REVERT: B 1119 ASN cc_start: 0.8572 (m-40) cc_final: 0.8352 (m110) REVERT: C 129 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7812 (mtmm) REVERT: C 169 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7256 (tm-30) REVERT: C 281 GLU cc_start: 0.8178 (mp0) cc_final: 0.7828 (mp0) REVERT: C 428 ASP cc_start: 0.7836 (p0) cc_final: 0.7505 (p0) REVERT: C 564 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: C 614 ASP cc_start: 0.7510 (t70) cc_final: 0.7254 (t70) REVERT: C 821 LEU cc_start: 0.8762 (tp) cc_final: 0.8544 (tt) REVERT: C 900 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8336 (mtm) REVERT: T 11 LYS cc_start: 0.8302 (tppp) cc_final: 0.8059 (tppp) outliers start: 88 outliers final: 62 residues processed: 639 average time/residue: 0.6514 time to fit residues: 478.6005 Evaluate side-chains 655 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 586 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 433 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 493 GLN 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 1144 GLU 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 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 377 PHE 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 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 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 120 VAL Chi-restraints excluded: chain C residue 385 THR 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 754 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 900 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 196 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 238 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 460 ASN A 501 ASN A 755 GLN 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 B 914 ASN C 30 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106515 restraints weight = 38994.953| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.34 r_work: 0.3346 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26433 Z= 0.159 Angle : 0.674 22.583 36085 Z= 0.338 Chirality : 0.048 0.632 4205 Planarity : 0.005 0.084 4581 Dihedral : 6.294 58.718 4529 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.89 % Allowed : 15.73 % 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: 0.04 (0.15), residues: 3140 helix: 2.21 (0.21), residues: 673 sheet: 0.92 (0.18), residues: 718 loop : -1.33 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.022 0.001 TYR C 265 PHE 0.025 0.001 PHE C 133 TRP 0.014 0.001 TRP C 886 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00381 (26333) covalent geometry : angle 0.64500 (35845) SS BOND : bond 0.00740 ( 42) SS BOND : angle 3.32776 ( 84) hydrogen bonds : bond 0.05956 ( 1023) hydrogen bonds : angle 4.87398 ( 2868) Misc. bond : bond 0.00038 ( 6) link_BETA1-4 : bond 0.00345 ( 15) link_BETA1-4 : angle 1.34007 ( 45) link_NAG-ASN : bond 0.00356 ( 37) link_NAG-ASN : angle 2.05980 ( 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 676 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 595 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8106 (m) cc_final: 0.7674 (t) REVERT: A 368 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8061 (tt) REVERT: A 374 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: A 414 GLN cc_start: 0.8591 (mm110) cc_final: 0.8375 (mp10) REVERT: A 465 GLU cc_start: 0.7649 (tp30) cc_final: 0.7288 (tp30) REVERT: A 675 GLN cc_start: 0.7910 (pp30) cc_final: 0.7650 (pp30) REVERT: A 787 GLN cc_start: 0.8385 (mt0) cc_final: 0.8081 (mt0) REVERT: A 1017 GLU cc_start: 0.8050 (tp30) cc_final: 0.7787 (tp30) REVERT: A 1072 GLU cc_start: 0.7982 (pm20) cc_final: 0.7743 (pm20) REVERT: B 97 LYS cc_start: 0.8117 (ptmm) cc_final: 0.7888 (ptmt) REVERT: B 147 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8053 (mtmm) REVERT: B 200 TYR cc_start: 0.8030 (m-10) cc_final: 0.7775 (m-80) REVERT: B 364 ASP cc_start: 0.7490 (t0) cc_final: 0.7096 (t0) REVERT: B 377 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: B 420 ASP cc_start: 0.7952 (m-30) cc_final: 0.7738 (m-30) REVERT: B 574 ASP cc_start: 0.8222 (t0) cc_final: 0.7803 (t0) REVERT: B 583 GLU cc_start: 0.7776 (tt0) cc_final: 0.7505 (tt0) REVERT: B 586 ASP cc_start: 0.7824 (m-30) cc_final: 0.7607 (m-30) REVERT: B 663 ASP cc_start: 0.7938 (t0) cc_final: 0.7711 (t0) REVERT: B 811 LYS cc_start: 0.7662 (tmtm) cc_final: 0.7273 (tmtm) REVERT: B 990 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6930 (mm-30) REVERT: B 1119 ASN cc_start: 0.8563 (m-40) cc_final: 0.8357 (m110) REVERT: C 169 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7254 (tm-30) REVERT: C 281 GLU cc_start: 0.8171 (mp0) cc_final: 0.7822 (mp0) REVERT: C 428 ASP cc_start: 0.7850 (p0) cc_final: 0.7517 (p0) REVERT: C 465 GLU cc_start: 0.8128 (tp30) cc_final: 0.7848 (mp0) REVERT: C 564 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: C 614 ASP cc_start: 0.7548 (t70) cc_final: 0.7262 (t70) REVERT: C 821 LEU cc_start: 0.8761 (tp) cc_final: 0.8542 (tt) outliers start: 81 outliers final: 63 residues processed: 634 average time/residue: 0.6469 time to fit residues: 471.2870 Evaluate side-chains 652 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 585 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 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 433 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 493 GLN 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 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 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 393 THR 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 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 1005 GLN 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 120 VAL Chi-restraints excluded: chain C residue 385 THR 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 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 780 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 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 285 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 283 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 439 ASN A 460 ASN A 501 ASN A 506 GLN A 710 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 563 GLN B 606 ASN B 914 ASN C 30 ASN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C1010 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106510 restraints weight = 38897.132| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.37 r_work: 0.3348 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26433 Z= 0.159 Angle : 0.685 22.418 36085 Z= 0.343 Chirality : 0.048 0.687 4205 Planarity : 0.005 0.085 4581 Dihedral : 6.299 58.690 4529 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 2.89 % Allowed : 15.94 % 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: 0.04 (0.15), residues: 3140 helix: 2.23 (0.21), residues: 673 sheet: 0.93 (0.18), residues: 717 loop : -1.34 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 319 TYR 0.022 0.001 TYR A 265 PHE 0.023 0.001 PHE C 133 TRP 0.014 0.001 TRP C 886 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00379 (26333) covalent geometry : angle 0.65113 (35845) SS BOND : bond 0.00740 ( 42) SS BOND : angle 3.40432 ( 84) hydrogen bonds : bond 0.05944 ( 1023) hydrogen bonds : angle 4.87090 ( 2868) Misc. bond : bond 0.00033 ( 6) link_BETA1-4 : bond 0.00347 ( 15) link_BETA1-4 : angle 1.33822 ( 45) link_NAG-ASN : bond 0.00319 ( 37) link_NAG-ASN : angle 2.47511 ( 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 669 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 588 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8114 (m) cc_final: 0.7690 (t) REVERT: A 368 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 374 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: A 414 GLN cc_start: 0.8580 (mm110) cc_final: 0.8378 (mp10) REVERT: A 465 GLU cc_start: 0.7652 (tp30) cc_final: 0.7292 (tp30) REVERT: A 675 GLN cc_start: 0.7926 (pp30) cc_final: 0.7663 (pp30) REVERT: A 787 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: A 1017 GLU cc_start: 0.8065 (tp30) cc_final: 0.7800 (tp30) REVERT: A 1072 GLU cc_start: 0.7985 (pm20) cc_final: 0.7740 (pm20) REVERT: B 97 LYS cc_start: 0.8146 (ptmm) cc_final: 0.7903 (ptmt) REVERT: B 147 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8038 (mtmm) REVERT: B 200 TYR cc_start: 0.7996 (m-10) cc_final: 0.7789 (m-80) REVERT: B 364 ASP cc_start: 0.7499 (t0) cc_final: 0.7103 (t0) REVERT: B 377 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: B 420 ASP cc_start: 0.7960 (m-30) cc_final: 0.7745 (m-30) REVERT: B 574 ASP cc_start: 0.8224 (t0) cc_final: 0.7815 (t0) REVERT: B 583 GLU cc_start: 0.7798 (tt0) cc_final: 0.7530 (tt0) REVERT: B 586 ASP cc_start: 0.7832 (m-30) cc_final: 0.7616 (m-30) REVERT: B 663 ASP cc_start: 0.7942 (t0) cc_final: 0.7701 (t0) REVERT: B 664 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 811 LYS cc_start: 0.7657 (tmtm) cc_final: 0.7286 (tmtm) REVERT: B 914 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7537 (p0) REVERT: B 976 VAL cc_start: 0.8352 (m) cc_final: 0.8138 (p) REVERT: B 990 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6571 (mm-30) REVERT: B 994 ASP cc_start: 0.7632 (m-30) cc_final: 0.7413 (m-30) REVERT: B 1119 ASN cc_start: 0.8565 (m-40) cc_final: 0.8361 (m110) REVERT: C 169 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 281 GLU cc_start: 0.8182 (mp0) cc_final: 0.7833 (mp0) REVERT: C 428 ASP cc_start: 0.7839 (p0) cc_final: 0.7514 (p0) REVERT: C 465 GLU cc_start: 0.8142 (tp30) cc_final: 0.7867 (mp0) REVERT: C 564 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: C 614 ASP cc_start: 0.7573 (t70) cc_final: 0.7264 (t70) REVERT: C 821 LEU cc_start: 0.8767 (tp) cc_final: 0.8546 (tt) REVERT: C 934 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7922 (mt) outliers start: 81 outliers final: 66 residues processed: 628 average time/residue: 0.6683 time to fit residues: 482.3256 Evaluate side-chains 657 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 583 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 97 LYS 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 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 433 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 710 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 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 143 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 393 THR 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 738 CYS 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 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 120 VAL Chi-restraints excluded: chain C residue 385 THR 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 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 780 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: 0.6980 chunk 58 optimal weight: 0.0980 chunk 162 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 460 ASN A 501 ASN A 506 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 969 ASN A1119 ASN B 271 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN C 30 ASN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106608 restraints weight = 38717.517| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.37 r_work: 0.3350 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 26433 Z= 0.226 Angle : 0.963 59.050 36085 Z= 0.538 Chirality : 0.052 1.127 4205 Planarity : 0.005 0.130 4581 Dihedral : 6.329 58.676 4529 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.24 % Favored : 95.57 % Rotamer: Outliers : 2.79 % Allowed : 16.05 % Favored : 81.17 % Cbeta Deviations : 0.07 % 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: 0.03 (0.15), residues: 3140 helix: 2.22 (0.21), residues: 673 sheet: 0.92 (0.18), residues: 717 loop : -1.34 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 319 TYR 0.022 0.001 TYR A 265 PHE 0.022 0.001 PHE C 133 TRP 0.012 0.001 TRP C 886 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00467 (26333) covalent geometry : angle 0.94119 (35845) SS BOND : bond 0.00709 ( 42) SS BOND : angle 3.35009 ( 84) hydrogen bonds : bond 0.05941 ( 1023) hydrogen bonds : angle 4.87115 ( 2868) Misc. bond : bond 0.00029 ( 6) link_BETA1-4 : bond 0.00344 ( 15) link_BETA1-4 : angle 1.33849 ( 45) link_NAG-ASN : bond 0.00317 ( 37) link_NAG-ASN : angle 2.44227 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11940.34 seconds wall clock time: 203 minutes 5.78 seconds (12185.78 seconds total)