Starting phenix.real_space_refine on Fri Mar 6 20:50:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whb_32498/03_2026/7whb_32498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whb_32498/03_2026/7whb_32498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whb_32498/03_2026/7whb_32498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whb_32498/03_2026/7whb_32498.map" model { file = "/net/cci-nas-00/data/ceres_data/7whb_32498/03_2026/7whb_32498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whb_32498/03_2026/7whb_32498.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 147 5.16 5 C 21677 2.51 5 N 5644 2.21 5 O 6741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34209 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "K" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} 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: "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: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 8.30, per 1000 atoms: 0.24 Number of scatterers: 34209 At special positions: 0 Unit cell: (166.881, 173.468, 248.125, 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 147 16.00 O 6741 8.00 N 5644 7.00 C 21677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " 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=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 616 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 282 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 616 " " NAG B1405 " - " ASN B 657 " " NAG C1201 " - " ASN A 282 " " NAG C1202 " - " ASN C 61 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 616 " " NAG C1207 " - " ASN C 657 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8054 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 78 sheets defined 18.4% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.021A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 5.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.043A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.500A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.988A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.829A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.615A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.853A 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 364 through 370 removed outlier: 4.037A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 5.108A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.511A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 939 removed outlier: 6.798A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.844A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.689A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.167A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.511A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.050A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 5.233A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.847A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (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: 3.683A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.841A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.083A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.666A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.576A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.058A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.575A pdb=" N GLN D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.952A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 197 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.938A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 197 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.942A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.670A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.198A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.854A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.556A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.690A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 removed outlier: 5.012A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.576A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.458A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.338A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.728A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.966A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.864A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.507A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.539A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.009A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.094A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.628A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.685A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.685A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.009A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.620A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.553A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.561A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.050A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.944A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.872A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.505A pdb=" N ASN D 59 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.505A pdb=" N ASN D 59 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 94 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.670A pdb=" N LYS D 151 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 188 " --> pdb=" O CYS D 148 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.670A pdb=" N LYS D 151 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 161 through 162 removed outlier: 3.595A pdb=" N VAL D 215 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.509A pdb=" N ARG E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.518A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.894A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.577A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.952A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.917A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 59 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.164A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.715A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER G 188 " --> pdb=" O CYS G 148 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.715A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS G 151 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU G 186 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.660A pdb=" N THR G 159 " --> pdb=" O ASN G 207 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G 217 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 215 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS G 208 " --> pdb=" O THR G 213 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.705A pdb=" N SER H 7 " --> pdb=" O SER H 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.527A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.900A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.582A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.964A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.685A pdb=" N TYR J 94 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.685A pdb=" N TYR J 94 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL J 110 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 128 through 132 removed outlier: 3.558A pdb=" N LYS J 151 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER J 188 " --> pdb=" O CYS J 148 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 128 through 132 removed outlier: 3.558A pdb=" N LYS J 151 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 158 through 162 removed outlier: 3.764A pdb=" N THR J 159 " --> pdb=" O ASN J 207 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN J 207 " --> pdb=" O THR J 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS J 217 " --> pdb=" O CYS J 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL J 215 " --> pdb=" O VAL J 206 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.791A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.541A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 114 through 118 removed outlier: 5.892A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.309A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN K 147 " --> pdb=" O GLU K 195 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU K 195 " --> pdb=" O GLN K 147 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA K 193 " --> pdb=" O LYS K 149 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3426 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: 8.87 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10928 1.35 - 1.47: 8827 1.47 - 1.59: 15013 1.59 - 1.72: 0 1.72 - 1.84: 183 Bond restraints: 34951 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.93e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG C1203 " pdb=" O5 NAG C1203 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 34946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 46611 1.98 - 3.96: 838 3.96 - 5.94: 69 5.94 - 7.92: 8 7.92 - 9.90: 4 Bond angle restraints: 47530 Sorted by residual: angle pdb=" N ILE C 418 " pdb=" CA ILE C 418 " pdb=" C ILE C 418 " ideal model delta sigma weight residual 113.47 108.63 4.84 1.01e+00 9.80e-01 2.30e+01 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 113.43 108.85 4.58 1.09e+00 8.42e-01 1.76e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.74 -5.04 1.22e+00 6.72e-01 1.71e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" N GLU C 281 " pdb=" CA GLU C 281 " pdb=" C GLU C 281 " ideal model delta sigma weight residual 114.75 109.99 4.76 1.26e+00 6.30e-01 1.43e+01 ... (remaining 47525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19628 17.98 - 35.96: 1541 35.96 - 53.94: 285 53.94 - 71.92: 66 71.92 - 89.90: 63 Dihedral angle restraints: 21583 sinusoidal: 9051 harmonic: 12532 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -0.65 -85.35 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -5.04 -80.96 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -8.49 -77.51 1 1.00e+01 1.00e-02 7.52e+01 ... (remaining 21580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 5534 0.136 - 0.272: 26 0.272 - 0.409: 0 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 5561 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 5558 not shown) Planarity restraints: 6108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 986 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 156 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO G 157 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.127 9.50e-02 1.11e+02 5.72e-02 2.66e+00 pdb=" NE ARG B 983 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " 0.000 2.00e-02 2.50e+03 ... (remaining 6105 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2232 2.73 - 3.28: 33511 3.28 - 3.82: 54324 3.82 - 4.36: 63317 4.36 - 4.90: 111731 Nonbonded interactions: 265115 Sorted by model distance: nonbonded pdb=" OH TYR C 674 " pdb=" N GLN C 690 " model vdw 2.193 3.120 nonbonded pdb=" NH1 ARG D 50 " pdb=" OE2 GLU D 99 " model vdw 2.200 3.120 nonbonded pdb=" CZ TYR C 674 " pdb=" N GLN C 690 " model vdw 2.220 3.340 nonbonded pdb=" O THR A 676 " pdb=" OG SER A 691 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG J 50 " pdb=" OE2 GLU J 99 " model vdw 2.252 3.120 ... (remaining 265110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 620 or resid 641 through 939 or resid 944 throu \ gh 1405)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1405)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1205)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.850 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.003 0.043 35057 Z= 0.161 Angle : 0.621 15.654 47794 Z= 0.317 Chirality : 0.045 0.681 5561 Planarity : 0.004 0.057 6072 Dihedral : 13.908 89.897 13376 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer: Outliers : 0.27 % Allowed : 0.29 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4265 helix: 2.02 (0.21), residues: 674 sheet: -0.59 (0.15), residues: 1314 loop : -1.54 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 983 TYR 0.023 0.001 TYR E 49 PHE 0.019 0.001 PHE C 906 TRP 0.016 0.001 TRP B 64 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00333 (34951) covalent geometry : angle 0.60144 (47530) SS BOND : bond 0.00484 ( 51) SS BOND : angle 1.25073 ( 102) hydrogen bonds : bond 0.22865 ( 1237) hydrogen bonds : angle 8.74390 ( 3426) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00529 ( 18) link_BETA1-4 : angle 1.99962 ( 54) link_NAG-ASN : bond 0.00425 ( 36) link_NAG-ASN : angle 2.85948 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 316 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8691 (p90) cc_final: 0.8349 (p90) REVERT: A 340 GLU cc_start: 0.8295 (pt0) cc_final: 0.8087 (pp20) REVERT: A 773 GLU cc_start: 0.7878 (tt0) cc_final: 0.7658 (tt0) REVERT: B 269 TYR cc_start: 0.8579 (m-80) cc_final: 0.8347 (m-80) REVERT: B 651 ILE cc_start: 0.9275 (pt) cc_final: 0.9012 (pp) REVERT: B 776 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8505 (ttpt) REVERT: B 780 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7949 (mp0) REVERT: B 1002 GLN cc_start: 0.8930 (tp40) cc_final: 0.8638 (tm-30) REVERT: B 1092 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7361 (pp20) REVERT: C 135 PHE cc_start: 0.8232 (m-80) cc_final: 0.8015 (m-80) REVERT: C 153 MET cc_start: 0.4122 (tpp) cc_final: 0.3600 (tpp) REVERT: C 780 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8079 (mp0) REVERT: C 814 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7513 (mmmt) REVERT: D 125 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8505 (tptp) REVERT: E 172 THR cc_start: 0.8627 (p) cc_final: 0.8282 (p) REVERT: E 210 ASN cc_start: 0.7705 (p0) cc_final: 0.7315 (p0) REVERT: H 210 ASN cc_start: 0.7779 (p0) cc_final: 0.7524 (p0) REVERT: K 210 ASN cc_start: 0.7932 (p0) cc_final: 0.7631 (p0) outliers start: 10 outliers final: 8 residues processed: 326 average time/residue: 0.5683 time to fit residues: 227.7913 Evaluate side-chains 246 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 128 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 343 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 343 ASN C 388 ASN C1005 GLN E 138 ASN E 166 GLN H 27 GLN H 138 ASN H 166 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.068490 restraints weight = 98925.765| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.84 r_work: 0.3093 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35057 Z= 0.207 Angle : 0.662 12.720 47794 Z= 0.331 Chirality : 0.046 0.483 5561 Planarity : 0.004 0.049 6072 Dihedral : 7.357 109.862 5777 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.27 % Favored : 92.71 % Rotamer: Outliers : 0.64 % Allowed : 7.98 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 4265 helix: 2.07 (0.21), residues: 676 sheet: -0.47 (0.14), residues: 1301 loop : -1.53 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 18 TYR 0.022 0.001 TYR A1067 PHE 0.017 0.001 PHE C 906 TRP 0.014 0.002 TRP C 104 HIS 0.003 0.001 HIS J 208 Details of bonding type rmsd covalent geometry : bond 0.00467 (34951) covalent geometry : angle 0.64670 (47530) SS BOND : bond 0.00619 ( 51) SS BOND : angle 1.40851 ( 102) hydrogen bonds : bond 0.04865 ( 1237) hydrogen bonds : angle 6.32375 ( 3426) Misc. bond : bond 0.00054 ( 1) link_BETA1-4 : bond 0.00477 ( 18) link_BETA1-4 : angle 1.66626 ( 54) link_NAG-ASN : bond 0.00323 ( 36) link_NAG-ASN : angle 2.61447 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9066 (t) cc_final: 0.8795 (m) REVERT: A 140 PHE cc_start: 0.8824 (p90) cc_final: 0.8393 (p90) REVERT: A 340 GLU cc_start: 0.9208 (pt0) cc_final: 0.8364 (pp20) REVERT: A 740 MET cc_start: 0.7416 (ttt) cc_final: 0.6327 (tmt) REVERT: A 1002 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 100 ILE cc_start: 0.8431 (pt) cc_final: 0.8016 (mp) REVERT: B 133 PHE cc_start: 0.7328 (m-80) cc_final: 0.6857 (m-80) REVERT: B 269 TYR cc_start: 0.8806 (m-80) cc_final: 0.8126 (m-80) REVERT: B 421 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.6480 (p90) REVERT: B 517 LEU cc_start: 0.8891 (tm) cc_final: 0.8669 (mm) REVERT: B 651 ILE cc_start: 0.8616 (pt) cc_final: 0.8306 (pp) REVERT: B 776 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8304 (ttpt) REVERT: B 780 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8223 (mp0) REVERT: B 1002 GLN cc_start: 0.9057 (tp40) cc_final: 0.8628 (tm-30) REVERT: C 135 PHE cc_start: 0.8644 (m-80) cc_final: 0.8388 (m-80) REVERT: C 153 MET cc_start: 0.4780 (tpp) cc_final: 0.4088 (tpp) REVERT: C 725 GLU cc_start: 0.8591 (tt0) cc_final: 0.8367 (tt0) REVERT: C 780 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8279 (mp0) REVERT: C 1050 MET cc_start: 0.9028 (ptm) cc_final: 0.8695 (ptm) REVERT: C 1092 GLU cc_start: 0.8099 (pp20) cc_final: 0.7881 (pp20) REVERT: D 81 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8396 (tpp) REVERT: E 137 ASN cc_start: 0.9112 (t0) cc_final: 0.8862 (t0) REVERT: E 172 THR cc_start: 0.9405 (p) cc_final: 0.9194 (p) REVERT: E 210 ASN cc_start: 0.8408 (p0) cc_final: 0.7838 (p0) REVERT: H 10 THR cc_start: 0.8412 (t) cc_final: 0.7495 (t) REVERT: H 79 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8093 (mp0) REVERT: H 82 ASP cc_start: 0.8883 (m-30) cc_final: 0.8438 (m-30) REVERT: H 122 ASP cc_start: 0.9352 (p0) cc_final: 0.8800 (p0) REVERT: H 210 ASN cc_start: 0.8628 (p0) cc_final: 0.8079 (p0) REVERT: K 81 GLU cc_start: 0.8992 (mp0) cc_final: 0.8730 (pm20) REVERT: K 82 ASP cc_start: 0.8432 (m-30) cc_final: 0.7939 (m-30) REVERT: K 137 ASN cc_start: 0.9159 (t0) cc_final: 0.8955 (t0) REVERT: K 187 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8806 (mm-30) REVERT: K 210 ASN cc_start: 0.8585 (p0) cc_final: 0.7682 (p0) outliers start: 24 outliers final: 9 residues processed: 292 average time/residue: 0.6130 time to fit residues: 218.5232 Evaluate side-chains 240 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 102 optimal weight: 4.9990 chunk 353 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 382 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 414 optimal weight: 3.9990 chunk 386 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.093517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070541 restraints weight = 100620.374| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 4.01 r_work: 0.3092 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35057 Z= 0.155 Angle : 0.631 13.104 47794 Z= 0.312 Chirality : 0.045 0.474 5561 Planarity : 0.004 0.045 6072 Dihedral : 6.572 56.791 5760 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.57 % Favored : 93.41 % Rotamer: Outliers : 1.12 % Allowed : 10.59 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 4265 helix: 2.10 (0.21), residues: 687 sheet: -0.40 (0.14), residues: 1328 loop : -1.47 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 18 TYR 0.020 0.001 TYR J 184 PHE 0.016 0.001 PHE B 106 TRP 0.016 0.001 TRP C 104 HIS 0.003 0.000 HIS J 208 Details of bonding type rmsd covalent geometry : bond 0.00350 (34951) covalent geometry : angle 0.61619 (47530) SS BOND : bond 0.00457 ( 51) SS BOND : angle 1.28002 ( 102) hydrogen bonds : bond 0.04132 ( 1237) hydrogen bonds : angle 5.80271 ( 3426) Misc. bond : bond 0.00027 ( 1) link_BETA1-4 : bond 0.00530 ( 18) link_BETA1-4 : angle 1.67764 ( 54) link_NAG-ASN : bond 0.00328 ( 36) link_NAG-ASN : angle 2.46206 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9043 (t) cc_final: 0.8819 (m) REVERT: A 140 PHE cc_start: 0.8851 (p90) cc_final: 0.8411 (p90) REVERT: A 740 MET cc_start: 0.7516 (ttt) cc_final: 0.6389 (tmt) REVERT: A 1002 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 92 PHE cc_start: 0.7986 (t80) cc_final: 0.7683 (t80) REVERT: B 100 ILE cc_start: 0.8442 (pt) cc_final: 0.8043 (mp) REVERT: B 269 TYR cc_start: 0.8835 (m-80) cc_final: 0.8145 (m-80) REVERT: B 421 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.6418 (p90) REVERT: B 651 ILE cc_start: 0.8626 (pt) cc_final: 0.8309 (pp) REVERT: B 776 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8330 (ttpt) REVERT: B 780 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8256 (mp0) REVERT: B 1002 GLN cc_start: 0.9045 (tp40) cc_final: 0.8652 (tm-30) REVERT: B 1092 GLU cc_start: 0.8454 (tp30) cc_final: 0.7897 (pp20) REVERT: C 153 MET cc_start: 0.4710 (tpp) cc_final: 0.4037 (tpp) REVERT: C 725 GLU cc_start: 0.8622 (tt0) cc_final: 0.8386 (tt0) REVERT: C 780 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8300 (mp0) REVERT: C 869 MET cc_start: 0.8752 (mtm) cc_final: 0.8470 (mtm) REVERT: C 1050 MET cc_start: 0.9088 (ptm) cc_final: 0.8817 (ptm) REVERT: C 1092 GLU cc_start: 0.8260 (pp20) cc_final: 0.7984 (pp20) REVERT: D 216 ASP cc_start: 0.8942 (m-30) cc_final: 0.8624 (t0) REVERT: D 220 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7425 (mm-30) REVERT: E 134 CYS cc_start: 0.8575 (t) cc_final: 0.8119 (t) REVERT: E 137 ASN cc_start: 0.9040 (t0) cc_final: 0.8735 (t0) REVERT: E 210 ASN cc_start: 0.8437 (p0) cc_final: 0.7864 (p0) REVERT: G 81 MET cc_start: 0.9171 (tmt) cc_final: 0.8964 (tpp) REVERT: G 82 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7868 (tm-30) REVERT: H 11 LEU cc_start: 0.9374 (tm) cc_final: 0.9173 (tt) REVERT: H 134 CYS cc_start: 0.8530 (t) cc_final: 0.8127 (t) REVERT: H 137 ASN cc_start: 0.9199 (t0) cc_final: 0.8959 (t0) REVERT: H 210 ASN cc_start: 0.8674 (p0) cc_final: 0.8092 (p0) REVERT: K 27 GLN cc_start: 0.8310 (mp10) cc_final: 0.8026 (mp10) REVERT: K 82 ASP cc_start: 0.8530 (m-30) cc_final: 0.8029 (m-30) REVERT: K 137 ASN cc_start: 0.9157 (t0) cc_final: 0.8926 (t0) REVERT: K 210 ASN cc_start: 0.8784 (p0) cc_final: 0.8541 (p0) outliers start: 42 outliers final: 19 residues processed: 284 average time/residue: 0.5700 time to fit residues: 199.9210 Evaluate side-chains 253 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 218 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 423 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 544 ASN B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.090139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067011 restraints weight = 101065.144| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.05 r_work: 0.3026 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 35057 Z= 0.332 Angle : 0.719 12.986 47794 Z= 0.360 Chirality : 0.048 0.510 5561 Planarity : 0.005 0.053 6072 Dihedral : 6.584 58.045 5759 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.32 % Allowed : 12.70 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4265 helix: 1.95 (0.21), residues: 694 sheet: -0.57 (0.14), residues: 1388 loop : -1.62 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 18 TYR 0.029 0.002 TYR E 49 PHE 0.021 0.002 PHE C 906 TRP 0.015 0.002 TRP G 36 HIS 0.007 0.001 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00756 (34951) covalent geometry : angle 0.70349 (47530) SS BOND : bond 0.00607 ( 51) SS BOND : angle 1.66700 ( 102) hydrogen bonds : bond 0.04689 ( 1237) hydrogen bonds : angle 5.71760 ( 3426) Misc. bond : bond 0.00101 ( 1) link_BETA1-4 : bond 0.00350 ( 18) link_BETA1-4 : angle 1.71199 ( 54) link_NAG-ASN : bond 0.00367 ( 36) link_NAG-ASN : angle 2.65819 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 233 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9119 (t) cc_final: 0.8895 (m) REVERT: A 140 PHE cc_start: 0.8851 (p90) cc_final: 0.8436 (p90) REVERT: A 740 MET cc_start: 0.7763 (ttt) cc_final: 0.6733 (tmt) REVERT: B 92 PHE cc_start: 0.8031 (t80) cc_final: 0.7611 (t80) REVERT: B 100 ILE cc_start: 0.8506 (pt) cc_final: 0.8112 (mp) REVERT: B 133 PHE cc_start: 0.7848 (m-80) cc_final: 0.6943 (m-80) REVERT: B 231 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9166 (mm) REVERT: B 269 TYR cc_start: 0.8865 (m-80) cc_final: 0.8127 (m-80) REVERT: B 421 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.6399 (p90) REVERT: B 651 ILE cc_start: 0.8679 (pt) cc_final: 0.8368 (pp) REVERT: B 776 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8315 (ttpt) REVERT: B 780 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8252 (mp0) REVERT: B 866 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7668 (p) REVERT: B 1002 GLN cc_start: 0.9054 (tp40) cc_final: 0.8654 (tm-30) REVERT: C 153 MET cc_start: 0.4523 (tpp) cc_final: 0.3977 (tpp) REVERT: C 725 GLU cc_start: 0.8655 (tt0) cc_final: 0.8452 (tt0) REVERT: C 780 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8268 (mp0) REVERT: C 1092 GLU cc_start: 0.8429 (pp20) cc_final: 0.8157 (pp20) REVERT: D 216 ASP cc_start: 0.8935 (m-30) cc_final: 0.8658 (t0) REVERT: E 11 LEU cc_start: 0.9466 (tm) cc_final: 0.9260 (tm) REVERT: E 33 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8907 (tp) REVERT: E 134 CYS cc_start: 0.8667 (t) cc_final: 0.8286 (t) REVERT: E 137 ASN cc_start: 0.9021 (t0) cc_final: 0.8778 (t0) REVERT: E 210 ASN cc_start: 0.8498 (p0) cc_final: 0.7908 (p0) REVERT: G 46 GLU cc_start: 0.8320 (tt0) cc_final: 0.7891 (tt0) REVERT: G 82 GLU cc_start: 0.8660 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 216 ASP cc_start: 0.9122 (m-30) cc_final: 0.8801 (t0) REVERT: H 210 ASN cc_start: 0.8691 (p0) cc_final: 0.8129 (p0) REVERT: K 82 ASP cc_start: 0.8637 (m-30) cc_final: 0.8319 (m-30) REVERT: K 137 ASN cc_start: 0.9114 (t0) cc_final: 0.8892 (t0) REVERT: K 210 ASN cc_start: 0.8785 (p0) cc_final: 0.8518 (p0) outliers start: 87 outliers final: 36 residues processed: 308 average time/residue: 0.5018 time to fit residues: 195.4718 Evaluate side-chains 254 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 384 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 335 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 421 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.092863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068641 restraints weight = 99280.459| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.83 r_work: 0.3092 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35057 Z= 0.143 Angle : 0.633 13.515 47794 Z= 0.311 Chirality : 0.046 0.475 5561 Planarity : 0.004 0.044 6072 Dihedral : 6.193 58.579 5759 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.92 % Allowed : 13.95 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 4265 helix: 2.02 (0.21), residues: 702 sheet: -0.44 (0.14), residues: 1381 loop : -1.51 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.024 0.001 TYR H 49 PHE 0.020 0.001 PHE B 65 TRP 0.018 0.001 TRP A 104 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00322 (34951) covalent geometry : angle 0.61899 (47530) SS BOND : bond 0.00446 ( 51) SS BOND : angle 1.33922 ( 102) hydrogen bonds : bond 0.03800 ( 1237) hydrogen bonds : angle 5.40020 ( 3426) Misc. bond : bond 0.00013 ( 1) link_BETA1-4 : bond 0.00616 ( 18) link_BETA1-4 : angle 1.67661 ( 54) link_NAG-ASN : bond 0.00328 ( 36) link_NAG-ASN : angle 2.40277 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 248 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8858 (p90) cc_final: 0.8454 (p90) REVERT: A 191 GLU cc_start: 0.8123 (pm20) cc_final: 0.7904 (mp0) REVERT: A 369 TYR cc_start: 0.8602 (t80) cc_final: 0.8328 (t80) REVERT: A 587 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9155 (pp) REVERT: A 725 GLU cc_start: 0.8833 (tt0) cc_final: 0.8590 (tt0) REVERT: A 740 MET cc_start: 0.7711 (ttt) cc_final: 0.6813 (tmt) REVERT: A 1002 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 92 PHE cc_start: 0.7906 (t80) cc_final: 0.7678 (t80) REVERT: B 100 ILE cc_start: 0.8494 (pt) cc_final: 0.8109 (mp) REVERT: B 133 PHE cc_start: 0.7768 (m-80) cc_final: 0.6979 (m-80) REVERT: B 269 TYR cc_start: 0.8863 (m-80) cc_final: 0.8134 (m-80) REVERT: B 421 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.6293 (p90) REVERT: B 651 ILE cc_start: 0.8647 (pt) cc_final: 0.8332 (pp) REVERT: B 776 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8294 (ttpt) REVERT: B 780 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8272 (mp0) REVERT: B 866 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7733 (p) REVERT: B 902 MET cc_start: 0.9008 (mmm) cc_final: 0.8776 (tpp) REVERT: B 1002 GLN cc_start: 0.9041 (tp40) cc_final: 0.8641 (tm-30) REVERT: C 153 MET cc_start: 0.4533 (tpp) cc_final: 0.3962 (tpp) REVERT: C 191 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: C 725 GLU cc_start: 0.8683 (tt0) cc_final: 0.8327 (tt0) REVERT: C 780 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8289 (mp0) REVERT: C 1092 GLU cc_start: 0.8452 (pp20) cc_final: 0.8161 (pp20) REVERT: D 216 ASP cc_start: 0.8767 (m-30) cc_final: 0.8551 (t0) REVERT: D 220 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7423 (mm-30) REVERT: E 134 CYS cc_start: 0.8412 (t) cc_final: 0.8017 (t) REVERT: E 137 ASN cc_start: 0.8945 (t0) cc_final: 0.8701 (t0) REVERT: E 210 ASN cc_start: 0.8462 (p0) cc_final: 0.7892 (p0) REVERT: G 46 GLU cc_start: 0.8239 (tt0) cc_final: 0.7799 (tt0) REVERT: G 82 GLU cc_start: 0.8642 (tm-30) cc_final: 0.7973 (tm-30) REVERT: G 216 ASP cc_start: 0.9047 (m-30) cc_final: 0.8739 (t0) REVERT: H 181 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8892 (pp) REVERT: H 182 SER cc_start: 0.9473 (OUTLIER) cc_final: 0.9057 (p) REVERT: H 185 ASP cc_start: 0.9542 (m-30) cc_final: 0.9210 (p0) REVERT: H 210 ASN cc_start: 0.8644 (p0) cc_final: 0.8054 (p0) REVERT: K 24 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8196 (ttm-80) REVERT: K 27 GLN cc_start: 0.8317 (mp10) cc_final: 0.8019 (mm-40) REVERT: K 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8063 (m-30) REVERT: K 210 ASN cc_start: 0.8759 (p0) cc_final: 0.8515 (p0) outliers start: 72 outliers final: 38 residues processed: 311 average time/residue: 0.5241 time to fit residues: 205.1688 Evaluate side-chains 283 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 4 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 371 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 338 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 67 optimal weight: 0.0570 chunk 363 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN D 207 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.092608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068364 restraints weight = 98948.807| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.83 r_work: 0.3085 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35057 Z= 0.159 Angle : 0.633 15.187 47794 Z= 0.311 Chirality : 0.045 0.467 5561 Planarity : 0.004 0.046 6072 Dihedral : 5.993 56.875 5759 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.11 % Allowed : 15.21 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4265 helix: 2.02 (0.21), residues: 702 sheet: -0.30 (0.14), residues: 1339 loop : -1.49 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 18 TYR 0.031 0.001 TYR J 153 PHE 0.014 0.001 PHE B 65 TRP 0.019 0.001 TRP C 104 HIS 0.002 0.000 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00363 (34951) covalent geometry : angle 0.61967 (47530) SS BOND : bond 0.00525 ( 51) SS BOND : angle 1.29961 ( 102) hydrogen bonds : bond 0.03767 ( 1237) hydrogen bonds : angle 5.27883 ( 3426) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00494 ( 18) link_BETA1-4 : angle 1.68262 ( 54) link_NAG-ASN : bond 0.00297 ( 36) link_NAG-ASN : angle 2.35431 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 249 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8858 (p90) cc_final: 0.8454 (p90) REVERT: A 369 TYR cc_start: 0.8551 (t80) cc_final: 0.8265 (t80) REVERT: A 725 GLU cc_start: 0.8846 (tt0) cc_final: 0.8546 (tt0) REVERT: A 740 MET cc_start: 0.7715 (ttt) cc_final: 0.6804 (tmt) REVERT: A 1002 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 92 PHE cc_start: 0.7980 (t80) cc_final: 0.7658 (t80) REVERT: B 100 ILE cc_start: 0.8552 (pt) cc_final: 0.8180 (mp) REVERT: B 118 LEU cc_start: 0.8408 (tt) cc_final: 0.7891 (mp) REVERT: B 131 CYS cc_start: 0.5279 (OUTLIER) cc_final: 0.1685 (p) REVERT: B 133 PHE cc_start: 0.7830 (m-80) cc_final: 0.5944 (m-80) REVERT: B 269 TYR cc_start: 0.8868 (m-80) cc_final: 0.8087 (m-80) REVERT: B 421 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.6275 (p90) REVERT: B 651 ILE cc_start: 0.8656 (pt) cc_final: 0.8352 (pp) REVERT: B 776 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8286 (ttpt) REVERT: B 780 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8273 (mp0) REVERT: B 866 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7690 (p) REVERT: B 1002 GLN cc_start: 0.9051 (tp40) cc_final: 0.8644 (tm-30) REVERT: C 153 MET cc_start: 0.4205 (tpp) cc_final: 0.3979 (tpp) REVERT: C 191 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: C 725 GLU cc_start: 0.8670 (tt0) cc_final: 0.8378 (tt0) REVERT: C 780 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8289 (mp0) REVERT: C 1092 GLU cc_start: 0.8501 (pp20) cc_final: 0.8209 (pp20) REVERT: D 220 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7396 (mm-30) REVERT: E 134 CYS cc_start: 0.8446 (t) cc_final: 0.8005 (t) REVERT: E 210 ASN cc_start: 0.8453 (p0) cc_final: 0.7871 (p0) REVERT: G 10 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7931 (mp0) REVERT: G 82 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8002 (tm-30) REVERT: G 184 TYR cc_start: 0.8010 (m-10) cc_final: 0.7684 (m-10) REVERT: G 216 ASP cc_start: 0.9034 (m-30) cc_final: 0.8702 (t0) REVERT: H 181 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8937 (pp) REVERT: H 182 SER cc_start: 0.9474 (OUTLIER) cc_final: 0.9047 (p) REVERT: H 185 ASP cc_start: 0.9550 (m-30) cc_final: 0.9305 (p0) REVERT: H 194 CYS cc_start: 0.6839 (p) cc_final: 0.6346 (p) REVERT: H 210 ASN cc_start: 0.8665 (p0) cc_final: 0.8089 (p0) REVERT: K 24 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8206 (ttm-80) REVERT: K 27 GLN cc_start: 0.8273 (mp10) cc_final: 0.7966 (mm-40) REVERT: K 70 ASP cc_start: 0.8931 (t70) cc_final: 0.8712 (t70) REVERT: K 82 ASP cc_start: 0.8667 (m-30) cc_final: 0.8076 (m-30) REVERT: K 210 ASN cc_start: 0.8766 (p0) cc_final: 0.8515 (p0) outliers start: 79 outliers final: 48 residues processed: 318 average time/residue: 0.5107 time to fit residues: 203.9956 Evaluate side-chains 288 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 63 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 384 optimal weight: 9.9990 chunk 265 optimal weight: 0.9980 chunk 399 optimal weight: 3.9990 chunk 262 optimal weight: 0.0770 chunk 198 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 293 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 129 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.094413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072080 restraints weight = 99435.008| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.89 r_work: 0.3116 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35057 Z= 0.110 Angle : 0.628 16.255 47794 Z= 0.305 Chirality : 0.045 0.445 5561 Planarity : 0.004 0.045 6072 Dihedral : 5.729 56.224 5759 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.71 % Allowed : 16.25 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4265 helix: 2.04 (0.21), residues: 704 sheet: -0.21 (0.14), residues: 1339 loop : -1.39 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 983 TYR 0.023 0.001 TYR J 153 PHE 0.013 0.001 PHE B 106 TRP 0.026 0.001 TRP C 104 HIS 0.002 0.000 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00247 (34951) covalent geometry : angle 0.61581 (47530) SS BOND : bond 0.00415 ( 51) SS BOND : angle 1.07027 ( 102) hydrogen bonds : bond 0.03362 ( 1237) hydrogen bonds : angle 5.09693 ( 3426) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00590 ( 18) link_BETA1-4 : angle 1.67607 ( 54) link_NAG-ASN : bond 0.00346 ( 36) link_NAG-ASN : angle 2.21251 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 260 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8876 (p90) cc_final: 0.8425 (p90) REVERT: A 369 TYR cc_start: 0.8592 (t80) cc_final: 0.8342 (t80) REVERT: A 725 GLU cc_start: 0.8870 (tt0) cc_final: 0.8582 (tt0) REVERT: A 740 MET cc_start: 0.7520 (ttt) cc_final: 0.6686 (tmt) REVERT: A 786 LYS cc_start: 0.9278 (mmmt) cc_final: 0.8930 (mppt) REVERT: B 92 PHE cc_start: 0.7938 (t80) cc_final: 0.7612 (t80) REVERT: B 100 ILE cc_start: 0.8582 (pt) cc_final: 0.8230 (mp) REVERT: B 131 CYS cc_start: 0.5226 (OUTLIER) cc_final: 0.1875 (p) REVERT: B 133 PHE cc_start: 0.7953 (m-80) cc_final: 0.6844 (m-80) REVERT: B 269 TYR cc_start: 0.8849 (m-80) cc_final: 0.8121 (m-80) REVERT: B 421 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.6163 (p90) REVERT: B 651 ILE cc_start: 0.8558 (pt) cc_final: 0.8244 (pp) REVERT: B 776 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8317 (ttpt) REVERT: B 780 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8162 (mp0) REVERT: B 866 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7630 (p) REVERT: B 902 MET cc_start: 0.9007 (mmm) cc_final: 0.8805 (tpp) REVERT: B 1002 GLN cc_start: 0.9034 (tp40) cc_final: 0.8670 (tm-30) REVERT: C 153 MET cc_start: 0.4228 (tpp) cc_final: 0.3993 (tpp) REVERT: C 191 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: C 269 TYR cc_start: 0.9035 (m-80) cc_final: 0.8611 (m-80) REVERT: C 489 TYR cc_start: 0.8935 (m-80) cc_final: 0.8723 (m-80) REVERT: C 697 MET cc_start: 0.8633 (ptp) cc_final: 0.8364 (ptm) REVERT: C 725 GLU cc_start: 0.8681 (tt0) cc_final: 0.8422 (tt0) REVERT: C 780 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8489 (mt-10) REVERT: C 1092 GLU cc_start: 0.8537 (pp20) cc_final: 0.8231 (pp20) REVERT: E 134 CYS cc_start: 0.8399 (t) cc_final: 0.7974 (t) REVERT: E 210 ASN cc_start: 0.8447 (p0) cc_final: 0.7866 (p0) REVERT: G 10 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7714 (mp0) REVERT: G 82 GLU cc_start: 0.8669 (tm-30) cc_final: 0.7964 (tm-30) REVERT: G 113 GLN cc_start: 0.9248 (pt0) cc_final: 0.8945 (pm20) REVERT: G 216 ASP cc_start: 0.9041 (m-30) cc_final: 0.8728 (t0) REVERT: H 93 ASN cc_start: 0.8518 (p0) cc_final: 0.8162 (t0) REVERT: H 181 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8950 (pp) REVERT: H 182 SER cc_start: 0.9492 (OUTLIER) cc_final: 0.9128 (p) REVERT: H 185 ASP cc_start: 0.9538 (m-30) cc_final: 0.9281 (p0) REVERT: H 194 CYS cc_start: 0.6894 (p) cc_final: 0.6621 (p) REVERT: H 210 ASN cc_start: 0.8670 (p0) cc_final: 0.8070 (p0) REVERT: J 203 ILE cc_start: 0.9622 (mp) cc_final: 0.8625 (mm) REVERT: K 27 GLN cc_start: 0.8468 (mp10) cc_final: 0.8054 (mm-40) REVERT: K 82 ASP cc_start: 0.8657 (m-30) cc_final: 0.8030 (m-30) REVERT: K 210 ASN cc_start: 0.8796 (p0) cc_final: 0.8544 (p0) outliers start: 64 outliers final: 42 residues processed: 315 average time/residue: 0.5384 time to fit residues: 213.0004 Evaluate side-chains 289 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 10 optimal weight: 3.9990 chunk 130 optimal weight: 0.0470 chunk 298 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 368 optimal weight: 0.9990 chunk 329 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.094361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072007 restraints weight = 98680.575| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.89 r_work: 0.3120 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35057 Z= 0.116 Angle : 0.628 14.814 47794 Z= 0.305 Chirality : 0.045 0.441 5561 Planarity : 0.004 0.051 6072 Dihedral : 5.658 56.426 5759 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.92 % Allowed : 16.46 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4265 helix: 2.03 (0.21), residues: 702 sheet: -0.18 (0.14), residues: 1339 loop : -1.35 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 24 TYR 0.033 0.001 TYR E 49 PHE 0.014 0.001 PHE A 135 TRP 0.031 0.001 TRP C 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00266 (34951) covalent geometry : angle 0.61491 (47530) SS BOND : bond 0.00404 ( 51) SS BOND : angle 1.43640 ( 102) hydrogen bonds : bond 0.03346 ( 1237) hydrogen bonds : angle 5.04122 ( 3426) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00542 ( 18) link_BETA1-4 : angle 1.64810 ( 54) link_NAG-ASN : bond 0.00309 ( 36) link_NAG-ASN : angle 2.18084 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 246 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8861 (p90) cc_final: 0.8434 (p90) REVERT: A 369 TYR cc_start: 0.8592 (t80) cc_final: 0.8343 (t80) REVERT: A 725 GLU cc_start: 0.8846 (tt0) cc_final: 0.8552 (tt0) REVERT: A 740 MET cc_start: 0.7525 (ttt) cc_final: 0.6598 (tmt) REVERT: A 786 LYS cc_start: 0.9311 (mmmt) cc_final: 0.8965 (mppt) REVERT: A 811 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7482 (mppt) REVERT: A 1002 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B 92 PHE cc_start: 0.7923 (t80) cc_final: 0.7596 (t80) REVERT: B 100 ILE cc_start: 0.8613 (pt) cc_final: 0.8271 (mp) REVERT: B 118 LEU cc_start: 0.8369 (tt) cc_final: 0.7854 (mp) REVERT: B 131 CYS cc_start: 0.5252 (OUTLIER) cc_final: 0.1594 (p) REVERT: B 133 PHE cc_start: 0.7938 (m-80) cc_final: 0.5885 (m-80) REVERT: B 269 TYR cc_start: 0.8863 (m-80) cc_final: 0.8125 (m-80) REVERT: B 421 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.6153 (p90) REVERT: B 651 ILE cc_start: 0.8559 (pt) cc_final: 0.8239 (pp) REVERT: B 776 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8312 (ttpt) REVERT: B 780 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8161 (mp0) REVERT: B 866 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7586 (p) REVERT: B 1002 GLN cc_start: 0.9030 (tp40) cc_final: 0.8640 (tm-30) REVERT: C 153 MET cc_start: 0.4211 (tpp) cc_final: 0.3988 (tpp) REVERT: C 191 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: C 269 TYR cc_start: 0.8996 (m-80) cc_final: 0.8711 (m-80) REVERT: C 697 MET cc_start: 0.8629 (ptp) cc_final: 0.8354 (ptm) REVERT: C 725 GLU cc_start: 0.8665 (tt0) cc_final: 0.8399 (tt0) REVERT: C 780 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8484 (mt-10) REVERT: C 1092 GLU cc_start: 0.8559 (pp20) cc_final: 0.8250 (pp20) REVERT: E 134 CYS cc_start: 0.8430 (t) cc_final: 0.7997 (t) REVERT: E 210 ASN cc_start: 0.8439 (p0) cc_final: 0.7858 (p0) REVERT: G 32 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6406 (t80) REVERT: G 82 GLU cc_start: 0.8595 (tm-30) cc_final: 0.7898 (tm-30) REVERT: G 113 GLN cc_start: 0.9211 (pt0) cc_final: 0.8890 (pm20) REVERT: G 216 ASP cc_start: 0.9033 (m-30) cc_final: 0.8708 (t0) REVERT: H 93 ASN cc_start: 0.8532 (p0) cc_final: 0.8221 (t0) REVERT: H 181 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8967 (pp) REVERT: H 182 SER cc_start: 0.9497 (OUTLIER) cc_final: 0.9128 (p) REVERT: H 185 ASP cc_start: 0.9537 (m-30) cc_final: 0.9269 (p0) REVERT: H 210 ASN cc_start: 0.8680 (p0) cc_final: 0.8071 (p0) REVERT: K 27 GLN cc_start: 0.8430 (mp10) cc_final: 0.8090 (mp10) REVERT: K 82 ASP cc_start: 0.8640 (m-30) cc_final: 0.8014 (m-30) REVERT: K 210 ASN cc_start: 0.8828 (p0) cc_final: 0.8564 (p0) outliers start: 72 outliers final: 47 residues processed: 307 average time/residue: 0.5378 time to fit residues: 206.9705 Evaluate side-chains 293 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 83 optimal weight: 8.9990 chunk 312 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 389 optimal weight: 0.9990 chunk 348 optimal weight: 0.4980 chunk 196 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.094339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071901 restraints weight = 98991.603| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.93 r_work: 0.3122 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35057 Z= 0.124 Angle : 0.635 14.740 47794 Z= 0.309 Chirality : 0.045 0.439 5561 Planarity : 0.004 0.061 6072 Dihedral : 5.615 56.361 5759 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.79 % Allowed : 17.16 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4265 helix: 2.00 (0.21), residues: 708 sheet: -0.18 (0.14), residues: 1340 loop : -1.34 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 18 TYR 0.021 0.001 TYR J 153 PHE 0.016 0.001 PHE C 135 TRP 0.036 0.001 TRP C 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00285 (34951) covalent geometry : angle 0.62260 (47530) SS BOND : bond 0.00410 ( 51) SS BOND : angle 1.39259 ( 102) hydrogen bonds : bond 0.03346 ( 1237) hydrogen bonds : angle 5.00936 ( 3426) Misc. bond : bond 0.00013 ( 1) link_BETA1-4 : bond 0.00565 ( 18) link_BETA1-4 : angle 1.64102 ( 54) link_NAG-ASN : bond 0.00297 ( 36) link_NAG-ASN : angle 2.16055 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8851 (p90) cc_final: 0.8426 (p90) REVERT: A 369 TYR cc_start: 0.8600 (t80) cc_final: 0.8347 (t80) REVERT: A 725 GLU cc_start: 0.8858 (tt0) cc_final: 0.8569 (tt0) REVERT: A 740 MET cc_start: 0.7514 (ttt) cc_final: 0.6585 (tmt) REVERT: A 786 LYS cc_start: 0.9312 (mmmt) cc_final: 0.8967 (mppt) REVERT: A 1002 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 66 HIS cc_start: 0.3534 (OUTLIER) cc_final: 0.2794 (p90) REVERT: B 92 PHE cc_start: 0.7902 (t80) cc_final: 0.7614 (t80) REVERT: B 100 ILE cc_start: 0.8521 (pt) cc_final: 0.8232 (mp) REVERT: B 118 LEU cc_start: 0.8356 (tt) cc_final: 0.7858 (mp) REVERT: B 131 CYS cc_start: 0.5289 (OUTLIER) cc_final: 0.1585 (p) REVERT: B 133 PHE cc_start: 0.7901 (m-80) cc_final: 0.5898 (m-80) REVERT: B 269 TYR cc_start: 0.8858 (m-80) cc_final: 0.8107 (m-80) REVERT: B 421 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.6116 (p90) REVERT: B 651 ILE cc_start: 0.8567 (pt) cc_final: 0.8247 (pp) REVERT: B 776 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8321 (ttpt) REVERT: B 780 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8133 (mp0) REVERT: B 866 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7590 (p) REVERT: B 977 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8726 (tm) REVERT: B 1002 GLN cc_start: 0.9025 (tp40) cc_final: 0.8639 (tm-30) REVERT: C 153 MET cc_start: 0.4325 (tpp) cc_final: 0.4086 (tpp) REVERT: C 191 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: C 269 TYR cc_start: 0.9014 (m-80) cc_final: 0.8719 (m-80) REVERT: C 489 TYR cc_start: 0.8924 (m-80) cc_final: 0.8695 (m-80) REVERT: C 697 MET cc_start: 0.8632 (ptp) cc_final: 0.8357 (ptm) REVERT: C 725 GLU cc_start: 0.8663 (tt0) cc_final: 0.8392 (tt0) REVERT: C 780 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8483 (mt-10) REVERT: C 1092 GLU cc_start: 0.8540 (pp20) cc_final: 0.8224 (pp20) REVERT: D 99 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: D 216 ASP cc_start: 0.8464 (t0) cc_final: 0.8153 (t0) REVERT: E 33 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8891 (tp) REVERT: E 134 CYS cc_start: 0.8431 (t) cc_final: 0.8011 (t) REVERT: E 210 ASN cc_start: 0.8411 (p0) cc_final: 0.7838 (p0) REVERT: G 10 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7702 (mp0) REVERT: G 82 GLU cc_start: 0.8646 (tm-30) cc_final: 0.7929 (tm-30) REVERT: G 113 GLN cc_start: 0.9196 (pt0) cc_final: 0.8870 (pm20) REVERT: G 216 ASP cc_start: 0.9025 (m-30) cc_final: 0.8707 (t0) REVERT: H 93 ASN cc_start: 0.8470 (p0) cc_final: 0.8222 (t0) REVERT: H 181 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8955 (pp) REVERT: H 182 SER cc_start: 0.9492 (OUTLIER) cc_final: 0.9124 (p) REVERT: H 185 ASP cc_start: 0.9521 (m-30) cc_final: 0.9258 (p0) REVERT: H 210 ASN cc_start: 0.8667 (p0) cc_final: 0.8053 (p0) REVERT: K 27 GLN cc_start: 0.8472 (mp10) cc_final: 0.8065 (mm-40) REVERT: K 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8014 (m-30) REVERT: K 210 ASN cc_start: 0.8824 (p0) cc_final: 0.8565 (p0) outliers start: 67 outliers final: 46 residues processed: 310 average time/residue: 0.5383 time to fit residues: 207.7573 Evaluate side-chains 295 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 39 optimal weight: 0.0870 chunk 412 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 224 optimal weight: 0.4980 chunk 347 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 405 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.094714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072200 restraints weight = 99367.970| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.99 r_work: 0.3138 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35057 Z= 0.116 Angle : 0.632 14.511 47794 Z= 0.308 Chirality : 0.045 0.434 5561 Planarity : 0.004 0.062 6072 Dihedral : 5.552 56.292 5759 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.79 % Allowed : 17.18 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4265 helix: 1.96 (0.21), residues: 713 sheet: -0.16 (0.14), residues: 1330 loop : -1.31 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 18 TYR 0.033 0.001 TYR J 153 PHE 0.014 0.001 PHE A 135 TRP 0.037 0.001 TRP C 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00265 (34951) covalent geometry : angle 0.62060 (47530) SS BOND : bond 0.00399 ( 51) SS BOND : angle 1.28397 ( 102) hydrogen bonds : bond 0.03269 ( 1237) hydrogen bonds : angle 4.95985 ( 3426) Misc. bond : bond 0.00009 ( 1) link_BETA1-4 : bond 0.00552 ( 18) link_BETA1-4 : angle 1.62975 ( 54) link_NAG-ASN : bond 0.00308 ( 36) link_NAG-ASN : angle 2.12281 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8841 (p90) cc_final: 0.8417 (p90) REVERT: A 369 TYR cc_start: 0.8584 (t80) cc_final: 0.8338 (t80) REVERT: A 725 GLU cc_start: 0.8862 (tt0) cc_final: 0.8280 (tt0) REVERT: A 740 MET cc_start: 0.7501 (ttt) cc_final: 0.6567 (tmt) REVERT: A 786 LYS cc_start: 0.9313 (mmmt) cc_final: 0.8977 (mppt) REVERT: A 1002 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 66 HIS cc_start: 0.3466 (OUTLIER) cc_final: 0.2729 (p90) REVERT: B 92 PHE cc_start: 0.7914 (t80) cc_final: 0.7633 (t80) REVERT: B 100 ILE cc_start: 0.8499 (pt) cc_final: 0.8205 (mp) REVERT: B 118 LEU cc_start: 0.8375 (tt) cc_final: 0.7871 (mp) REVERT: B 131 CYS cc_start: 0.5274 (OUTLIER) cc_final: 0.1586 (p) REVERT: B 133 PHE cc_start: 0.7869 (m-80) cc_final: 0.5893 (m-80) REVERT: B 269 TYR cc_start: 0.8862 (m-80) cc_final: 0.8126 (m-80) REVERT: B 369 TYR cc_start: 0.9071 (t80) cc_final: 0.8709 (t80) REVERT: B 421 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.6120 (p90) REVERT: B 651 ILE cc_start: 0.8609 (pt) cc_final: 0.8283 (pp) REVERT: B 776 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8335 (ttpt) REVERT: B 780 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8083 (mp0) REVERT: B 866 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7633 (p) REVERT: B 977 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8790 (tm) REVERT: B 1002 GLN cc_start: 0.9025 (tp40) cc_final: 0.8607 (tm-30) REVERT: B 1092 GLU cc_start: 0.8370 (tp30) cc_final: 0.7817 (pp20) REVERT: C 153 MET cc_start: 0.4305 (tpp) cc_final: 0.4073 (tpp) REVERT: C 191 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: C 269 TYR cc_start: 0.9030 (m-80) cc_final: 0.8778 (m-80) REVERT: C 489 TYR cc_start: 0.8919 (m-80) cc_final: 0.8698 (m-80) REVERT: C 697 MET cc_start: 0.8642 (ptp) cc_final: 0.8371 (ptm) REVERT: C 725 GLU cc_start: 0.8659 (tt0) cc_final: 0.8390 (tt0) REVERT: C 780 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8481 (mt-10) REVERT: C 1092 GLU cc_start: 0.8547 (pp20) cc_final: 0.8232 (pp20) REVERT: E 33 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8885 (tp) REVERT: E 134 CYS cc_start: 0.8408 (t) cc_final: 0.7974 (t) REVERT: E 210 ASN cc_start: 0.8399 (p0) cc_final: 0.7827 (p0) REVERT: G 3 GLN cc_start: 0.8449 (mm110) cc_final: 0.8202 (mm-40) REVERT: G 10 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7682 (mp0) REVERT: G 32 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6351 (t80) REVERT: G 82 GLU cc_start: 0.8646 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 113 GLN cc_start: 0.9171 (pt0) cc_final: 0.8831 (pm20) REVERT: G 156 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8501 (mm-30) REVERT: G 184 TYR cc_start: 0.7908 (m-10) cc_final: 0.7696 (m-10) REVERT: G 216 ASP cc_start: 0.8999 (m-30) cc_final: 0.8691 (t0) REVERT: H 181 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8937 (pp) REVERT: H 182 SER cc_start: 0.9475 (OUTLIER) cc_final: 0.9091 (p) REVERT: H 185 ASP cc_start: 0.9515 (m-30) cc_final: 0.9256 (p0) REVERT: H 210 ASN cc_start: 0.8652 (p0) cc_final: 0.8037 (p0) REVERT: J 179 GLN cc_start: 0.8952 (mt0) cc_final: 0.8695 (mp10) REVERT: K 27 GLN cc_start: 0.8490 (mp10) cc_final: 0.8133 (mm-40) REVERT: K 82 ASP cc_start: 0.8633 (m-30) cc_final: 0.8009 (m-30) REVERT: K 210 ASN cc_start: 0.8801 (p0) cc_final: 0.8552 (p0) outliers start: 67 outliers final: 50 residues processed: 307 average time/residue: 0.5269 time to fit residues: 202.9691 Evaluate side-chains 302 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 98 optimal weight: 0.8980 chunk 410 optimal weight: 0.0770 chunk 220 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 414 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.094384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070530 restraints weight = 98773.629| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.81 r_work: 0.3134 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35057 Z= 0.131 Angle : 0.637 14.363 47794 Z= 0.312 Chirality : 0.045 0.435 5561 Planarity : 0.004 0.063 6072 Dihedral : 5.546 56.441 5759 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.76 % Allowed : 17.21 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4265 helix: 1.96 (0.21), residues: 713 sheet: -0.16 (0.14), residues: 1340 loop : -1.30 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 18 TYR 0.023 0.001 TYR H 49 PHE 0.016 0.001 PHE C 135 TRP 0.036 0.001 TRP C 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00303 (34951) covalent geometry : angle 0.62550 (47530) SS BOND : bond 0.00400 ( 51) SS BOND : angle 1.28284 ( 102) hydrogen bonds : bond 0.03326 ( 1237) hydrogen bonds : angle 4.95407 ( 3426) Misc. bond : bond 0.00019 ( 1) link_BETA1-4 : bond 0.00549 ( 18) link_BETA1-4 : angle 1.64113 ( 54) link_NAG-ASN : bond 0.00288 ( 36) link_NAG-ASN : angle 2.12467 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13930.40 seconds wall clock time: 236 minutes 57.63 seconds (14217.63 seconds total)