Starting phenix.real_space_refine on Fri Feb 6 15:09:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9og7_70455/02_2026/9og7_70455.cif Found real_map, /net/cci-nas-00/data/ceres_data/9og7_70455/02_2026/9og7_70455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9og7_70455/02_2026/9og7_70455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9og7_70455/02_2026/9og7_70455.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9og7_70455/02_2026/9og7_70455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9og7_70455/02_2026/9og7_70455.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 16146 2.51 5 N 4130 2.21 5 O 5004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25396 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8320 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 7 Chain: "C" Number of atoms: 7919 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1012, 7905 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 56, 'TRANS': 955} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1012, 7905 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 56, 'TRANS': 955} Chain breaks: 7 bond proxies already assigned to first conformer: 8072 Chain: "B" Number of atoms: 8223 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1051, 8214 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 58, 'TRANS': 992} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1051, 8214 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 58, 'TRANS': 992} Chain breaks: 7 bond proxies already assigned to first conformer: 8394 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "c" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 8.66, per 1000 atoms: 0.34 Number of scatterers: 25396 At special positions: 0 Unit cell: (131.456, 133.952, 192.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 5004 8.00 N 4130 7.00 C 16146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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 705 " - pdb=" SG CYS C 883 " 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 A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS B 883 " 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.07 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG S 2 " - " BMA S 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 125 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 164 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 17 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1074 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 709 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN C 282 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG a 1 " - " ASN B 234 " " NAG c 1 " - " ASN C 343 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5882 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 45 sheets defined 24.7% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.869A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.694A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 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 759 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 850 through 855 removed outlier: 4.001A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.628A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.052A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 947 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.952A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.500A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.692A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.765A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 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 759 through 783 removed outlier: 3.660A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.593A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.531A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.745A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.627A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.855A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 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 371 removed outlier: 3.954A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.346A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.966A pdb=" N HIS B 625 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 626 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP B 627 " --> pdb=" O ILE B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.770A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.613A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.593A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.533A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.233A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.883A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.598A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.570A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.085A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.404A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.662A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.776A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 319 removed outlier: 4.270A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.954A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.999A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.538A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.452A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.641A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.779A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AB9, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AC1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.955A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 325 through 326 removed outlier: 5.274A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.619A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.793A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.526A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.822A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.348A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.348A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.093A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.894A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.975A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.411A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AD9, first strand: chain 'B' and resid 310 through 315 removed outlier: 4.568A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.561A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.547A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.279A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.279A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.447A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1120 through 1122 942 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7979 1.34 - 1.46: 6278 1.46 - 1.58: 11566 1.58 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 25964 Sorted by residual: bond pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.25e+01 bond pdb=" N ASN C 234 " pdb=" CA ASN C 234 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.21e-02 6.83e+03 1.11e+01 bond pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.31e+00 bond pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.22e-02 6.72e+03 7.17e+00 bond pdb=" N ILE C 235 " pdb=" CA ILE C 235 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.19e-02 7.06e+03 6.72e+00 ... (remaining 25959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 34912 2.21 - 4.43: 382 4.43 - 6.64: 44 6.64 - 8.86: 11 8.86 - 11.07: 2 Bond angle restraints: 35351 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.15 106.72 6.43 1.19e+00 7.06e-01 2.92e+01 angle pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" C CYS B 617 " ideal model delta sigma weight residual 110.80 121.87 -11.07 2.13e+00 2.20e-01 2.70e+01 angle pdb=" C ALA A 570 " pdb=" CA ALA A 570 " pdb=" CB ALA A 570 " ideal model delta sigma weight residual 116.54 110.96 5.58 1.15e+00 7.56e-01 2.35e+01 angle pdb=" O ASN B 616 " pdb=" C ASN B 616 " pdb=" N CYS B 617 " ideal model delta sigma weight residual 122.59 128.83 -6.24 1.33e+00 5.65e-01 2.20e+01 angle pdb=" N THR C 236 " pdb=" CA THR C 236 " pdb=" C THR C 236 " ideal model delta sigma weight residual 113.72 107.70 6.02 1.30e+00 5.92e-01 2.14e+01 ... (remaining 35346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.83: 14806 23.83 - 47.67: 1323 47.67 - 71.50: 229 71.50 - 95.34: 38 95.34 - 119.17: 6 Dihedral angle restraints: 16402 sinusoidal: 7272 harmonic: 9130 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -174.28 88.28 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " pdb=" SG CYS C 883 " pdb=" CB CYS C 883 " ideal model delta sinusoidal sigma weight residual 93.00 -179.38 -87.62 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C 705 " pdb=" SG CYS C 705 " pdb=" SG CYS B 883 " pdb=" CB CYS B 883 " ideal model delta sinusoidal sigma weight residual 93.00 26.76 66.24 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 16399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 4194 0.148 - 0.296: 15 0.296 - 0.444: 5 0.444 - 0.592: 1 0.592 - 0.739: 1 Chirality restraints: 4216 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.97e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 ... (remaining 4213 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " 0.336 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG B1307 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.248 2.00e-02 2.50e+03 2.08e-01 5.41e+02 pdb=" C7 NAG R 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.350 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.181 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG A1305 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.248 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " 0.142 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 10342 2.90 - 3.40: 22554 3.40 - 3.90: 42027 3.90 - 4.40: 48071 4.40 - 4.90: 82152 Nonbonded interactions: 205146 Sorted by model distance: nonbonded pdb=" N ASN A 282 " pdb=" OD1 ASN A 282 " model vdw 2.398 3.120 nonbonded pdb=" N THR B 618 " pdb=" OG1 THR B 618 " model vdw 2.486 2.496 nonbonded pdb=" C4 NAG F 2 " pdb=" O5 BMA F 3 " model vdw 2.489 2.776 nonbonded pdb=" OG1 THR C 108 " pdb=" O7 NAG R 1 " model vdw 2.494 3.040 nonbonded pdb=" O LEU A 849 " pdb=" O ILE A 850 " model vdw 2.508 3.040 ... (remaining 205141 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 25 through 66 or resid 79 through 140 or resid 157 through \ 176 or resid 190 through 243 or resid 263 through 443 or resid 450 through 621 \ or resid 640 through 827 or resid 852 through 954 or resid 956 through 1137 or r \ esid 1139 through 1302)) selection = (chain 'B' and (resid 25 through 66 or resid 79 through 140 or resid 157 through \ 176 or resid 190 through 243 or resid 263 through 443 or resid 450 through 621 \ or resid 640 through 827 or resid 852 through 954 or resid 956 through 1137 or r \ esid 1139 through 1302)) selection = (chain 'C' and (resid 25 through 176 or resid 190 through 443 or resid 450 throu \ gh 954 or resid 956 through 1137 or resid 1139 through 1302)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.710 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 0.046 26074 Z= 0.136 Angle : 0.631 15.586 35639 Z= 0.319 Chirality : 0.048 0.739 4216 Planarity : 0.007 0.291 4497 Dihedral : 17.243 119.170 10394 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.65 % Favored : 92.96 % Rotamer: Outliers : 4.11 % Allowed : 27.23 % Favored : 68.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.15), residues: 3085 helix: 1.26 (0.21), residues: 668 sheet: -0.60 (0.20), residues: 598 loop : -1.80 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.017 0.001 TYR B1067 PHE 0.037 0.001 PHE C 106 TRP 0.009 0.001 TRP B 886 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00266 (25964) covalent geometry : angle 0.57763 (35351) SS BOND : bond 0.00658 ( 42) SS BOND : angle 1.34786 ( 84) hydrogen bonds : bond 0.13573 ( 916) hydrogen bonds : angle 7.38976 ( 2598) link_BETA1-3 : bond 0.00520 ( 1) link_BETA1-3 : angle 1.39094 ( 3) link_BETA1-4 : bond 0.00990 ( 27) link_BETA1-4 : angle 2.03288 ( 81) link_NAG-ASN : bond 0.00772 ( 40) link_NAG-ASN : angle 3.95878 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 231 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5199 (OUTLIER) cc_final: 0.4458 (t70) REVERT: A 97 LYS cc_start: 0.4498 (OUTLIER) cc_final: 0.3109 (mptt) REVERT: A 131 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5082 (m) REVERT: A 133 PHE cc_start: 0.5346 (OUTLIER) cc_final: 0.3212 (p90) REVERT: A 281 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: A 346 ARG cc_start: 0.4579 (OUTLIER) cc_final: 0.4081 (mtm-85) REVERT: A 464 PHE cc_start: 0.1845 (OUTLIER) cc_final: 0.0951 (t80) REVERT: A 574 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: A 619 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 675 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: A 814 LYS cc_start: 0.8282 (mptt) cc_final: 0.7878 (mtpp) REVERT: A 854 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8162 (mmmt) REVERT: A 1031 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: A 1101 HIS cc_start: 0.7627 (m90) cc_final: 0.7362 (m90) REVERT: C 41 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8377 (mtpt) REVERT: C 45 SER cc_start: 0.8401 (t) cc_final: 0.8121 (p) REVERT: C 133 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.5644 (p90) REVERT: C 169 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 191 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8367 (mt-10) REVERT: C 347 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6891 (t80) REVERT: C 409 GLN cc_start: 0.8245 (mp-120) cc_final: 0.7803 (mm-40) REVERT: C 448 ASN cc_start: 0.7279 (m110) cc_final: 0.6998 (m110) REVERT: C 453 TYR cc_start: 0.7614 (p90) cc_final: 0.6650 (p90) REVERT: C 493 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6760 (tm-30) REVERT: C 590 CYS cc_start: 0.6385 (OUTLIER) cc_final: 0.6123 (m) REVERT: C 854 LYS cc_start: 0.7668 (mttp) cc_final: 0.7416 (mtmm) REVERT: C 894 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 96 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6118 (pp20) REVERT: B 99 ASN cc_start: 0.6587 (m-40) cc_final: 0.6066 (t0) REVERT: B 187 LYS cc_start: 0.5317 (OUTLIER) cc_final: 0.4675 (tppt) REVERT: B 360 ASN cc_start: 0.7549 (t0) cc_final: 0.7243 (m-40) REVERT: B 420 ASP cc_start: 0.7629 (m-30) cc_final: 0.7365 (m-30) REVERT: B 516 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: B 633 TRP cc_start: 0.8900 (OUTLIER) cc_final: 0.8580 (m100) REVERT: B 751 ASN cc_start: 0.8468 (m-40) cc_final: 0.8238 (m-40) REVERT: B 774 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7548 (mp-120) REVERT: B 780 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7730 (mm-30) REVERT: B 811 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6994 (ptpp) REVERT: B 868 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: B 988 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7615 (mp0) outliers start: 112 outliers final: 76 residues processed: 320 average time/residue: 0.1619 time to fit residues: 84.7046 Evaluate side-chains 321 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 224 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.185888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133221 restraints weight = 43232.382| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.67 r_work: 0.2972 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26074 Z= 0.194 Angle : 0.656 14.860 35639 Z= 0.317 Chirality : 0.048 0.386 4216 Planarity : 0.004 0.044 4497 Dihedral : 9.736 109.039 4944 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.33 % Favored : 92.28 % Rotamer: Outliers : 5.53 % Allowed : 25.37 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -1.23 (0.15), residues: 3085 helix: 1.21 (0.21), residues: 678 sheet: -0.53 (0.21), residues: 591 loop : -1.80 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.024 0.001 TYR C1067 PHE 0.019 0.001 PHE A 392 TRP 0.009 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00476 (25964) covalent geometry : angle 0.60718 (35351) SS BOND : bond 0.00638 ( 42) SS BOND : angle 1.42175 ( 84) hydrogen bonds : bond 0.04424 ( 916) hydrogen bonds : angle 5.84334 ( 2598) link_BETA1-3 : bond 0.00488 ( 1) link_BETA1-3 : angle 1.44286 ( 3) link_BETA1-4 : bond 0.00465 ( 27) link_BETA1-4 : angle 1.67165 ( 81) link_NAG-ASN : bond 0.00626 ( 40) link_NAG-ASN : angle 3.99480 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 218 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8280 (m-10) cc_final: 0.8018 (m-10) REVERT: A 66 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.4517 (t70) REVERT: A 97 LYS cc_start: 0.4633 (OUTLIER) cc_final: 0.3236 (mptt) REVERT: A 131 CYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5421 (m) REVERT: A 133 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.3334 (p90) REVERT: A 281 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6716 (pt0) REVERT: A 309 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: A 346 ARG cc_start: 0.4742 (OUTLIER) cc_final: 0.4298 (mtm-85) REVERT: A 408 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.4436 (tpm170) REVERT: A 492 LEU cc_start: 0.1570 (OUTLIER) cc_final: 0.1266 (mm) REVERT: A 564 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: A 574 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 619 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7667 (mm-30) REVERT: A 675 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: A 814 LYS cc_start: 0.8540 (mptt) cc_final: 0.7997 (mtpt) REVERT: A 1031 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: A 1101 HIS cc_start: 0.7769 (m90) cc_final: 0.7403 (m90) REVERT: C 133 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.5573 (p90) REVERT: C 191 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8555 (mt-10) REVERT: C 211 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.6365 (p0) REVERT: C 239 GLN cc_start: 0.8459 (tt0) cc_final: 0.7947 (mt0) REVERT: C 347 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6896 (t80) REVERT: C 409 GLN cc_start: 0.8217 (mp-120) cc_final: 0.7767 (mm-40) REVERT: C 448 ASN cc_start: 0.7330 (m110) cc_final: 0.7011 (m-40) REVERT: C 453 TYR cc_start: 0.7635 (p90) cc_final: 0.6672 (p90) REVERT: C 493 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6653 (tm-30) REVERT: C 516 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6685 (mm-30) REVERT: C 675 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: C 854 LYS cc_start: 0.7886 (mttp) cc_final: 0.7579 (mtmm) REVERT: C 1031 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: B 96 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6099 (pp20) REVERT: B 187 LYS cc_start: 0.5187 (OUTLIER) cc_final: 0.4522 (tppt) REVERT: B 215 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6924 (p0) REVERT: B 360 ASN cc_start: 0.7715 (t0) cc_final: 0.7319 (m-40) REVERT: B 420 ASP cc_start: 0.7735 (m-30) cc_final: 0.7436 (m-30) REVERT: B 456 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.6689 (p90) REVERT: B 633 TRP cc_start: 0.8947 (OUTLIER) cc_final: 0.8498 (m100) REVERT: B 747 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7895 (m) REVERT: B 751 ASN cc_start: 0.8561 (m-40) cc_final: 0.8277 (m-40) REVERT: B 774 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7771 (mp-120) REVERT: B 811 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6968 (ptpp) REVERT: B 868 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: B 955 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7202 (m-40) REVERT: B 988 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7701 (mp0) outliers start: 151 outliers final: 86 residues processed: 355 average time/residue: 0.1436 time to fit residues: 83.5748 Evaluate side-chains 324 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 209 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.186356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130849 restraints weight = 34641.632| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.40 r_work: 0.3050 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26074 Z= 0.131 Angle : 0.607 14.916 35639 Z= 0.293 Chirality : 0.047 0.388 4216 Planarity : 0.004 0.045 4497 Dihedral : 9.303 108.656 4892 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.78 % Favored : 92.83 % Rotamer: Outliers : 4.73 % Allowed : 26.28 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.15), residues: 3085 helix: 1.62 (0.21), residues: 667 sheet: -0.42 (0.20), residues: 615 loop : -1.79 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.001 PHE C 168 TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00306 (25964) covalent geometry : angle 0.55930 (35351) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.26219 ( 84) hydrogen bonds : bond 0.03818 ( 916) hydrogen bonds : angle 5.51781 ( 2598) link_BETA1-3 : bond 0.00470 ( 1) link_BETA1-3 : angle 1.40862 ( 3) link_BETA1-4 : bond 0.00455 ( 27) link_BETA1-4 : angle 1.65856 ( 81) link_NAG-ASN : bond 0.00607 ( 40) link_NAG-ASN : angle 3.78920 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 227 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4851 (OUTLIER) cc_final: 0.4201 (t70) REVERT: A 97 LYS cc_start: 0.4450 (OUTLIER) cc_final: 0.3169 (mptt) REVERT: A 131 CYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5157 (m) REVERT: A 133 PHE cc_start: 0.5672 (OUTLIER) cc_final: 0.3370 (p90) REVERT: A 314 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: A 346 ARG cc_start: 0.4900 (OUTLIER) cc_final: 0.4271 (mtm-85) REVERT: A 464 PHE cc_start: 0.1943 (OUTLIER) cc_final: 0.0838 (t80) REVERT: A 492 LEU cc_start: 0.1655 (OUTLIER) cc_final: 0.1394 (mm) REVERT: A 569 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6247 (mt) REVERT: A 574 ASP cc_start: 0.7468 (m-30) cc_final: 0.7088 (m-30) REVERT: A 619 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 675 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6645 (mt0) REVERT: A 814 LYS cc_start: 0.8491 (mptt) cc_final: 0.7927 (mtpt) REVERT: A 947 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7086 (mtmt) REVERT: A 1031 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: A 1101 HIS cc_start: 0.7706 (m90) cc_final: 0.7318 (m90) REVERT: C 133 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.5361 (p90) REVERT: C 191 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8397 (mt-10) REVERT: C 347 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6938 (t80) REVERT: C 409 GLN cc_start: 0.8160 (mp-120) cc_final: 0.7754 (mm-40) REVERT: C 448 ASN cc_start: 0.7175 (m110) cc_final: 0.6841 (m-40) REVERT: C 493 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: C 516 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6571 (mm-30) REVERT: C 675 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: C 854 LYS cc_start: 0.7844 (mttp) cc_final: 0.7503 (mtmm) REVERT: C 1031 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: B 96 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6015 (pp20) REVERT: B 99 ASN cc_start: 0.6506 (m-40) cc_final: 0.5889 (t0) REVERT: B 187 LYS cc_start: 0.5073 (OUTLIER) cc_final: 0.4456 (tppt) REVERT: B 360 ASN cc_start: 0.7698 (t0) cc_final: 0.7275 (m-40) REVERT: B 420 ASP cc_start: 0.7626 (m-30) cc_final: 0.7279 (m-30) REVERT: B 456 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6501 (p90) REVERT: B 633 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.8435 (m100) REVERT: B 747 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7802 (m) REVERT: B 751 ASN cc_start: 0.8485 (m-40) cc_final: 0.8187 (m-40) REVERT: B 774 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7727 (mp-120) REVERT: B 780 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7967 (mm-30) REVERT: B 811 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6926 (ptpp) REVERT: B 868 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 955 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7061 (m-40) REVERT: B 988 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7850 (mp0) outliers start: 129 outliers final: 76 residues processed: 337 average time/residue: 0.1556 time to fit residues: 85.6061 Evaluate side-chains 320 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 217 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 907 ASN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.185982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132091 restraints weight = 44232.190| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.64 r_work: 0.3017 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26074 Z= 0.174 Angle : 0.630 15.049 35639 Z= 0.304 Chirality : 0.048 0.387 4216 Planarity : 0.004 0.045 4497 Dihedral : 9.222 108.969 4878 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.27 % Favored : 92.38 % Rotamer: Outliers : 6.01 % Allowed : 25.01 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.15), residues: 3085 helix: 1.51 (0.21), residues: 674 sheet: -0.42 (0.20), residues: 612 loop : -1.82 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.022 0.001 TYR C1067 PHE 0.026 0.001 PHE C 106 TRP 0.009 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00423 (25964) covalent geometry : angle 0.58348 (35351) SS BOND : bond 0.00528 ( 42) SS BOND : angle 1.29674 ( 84) hydrogen bonds : bond 0.04136 ( 916) hydrogen bonds : angle 5.47872 ( 2598) link_BETA1-3 : bond 0.00504 ( 1) link_BETA1-3 : angle 1.43831 ( 3) link_BETA1-4 : bond 0.00465 ( 27) link_BETA1-4 : angle 1.65576 ( 81) link_NAG-ASN : bond 0.00584 ( 40) link_NAG-ASN : angle 3.81151 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 214 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5211 (OUTLIER) cc_final: 0.4455 (t70) REVERT: A 97 LYS cc_start: 0.4523 (OUTLIER) cc_final: 0.3193 (mptt) REVERT: A 131 CYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5178 (m) REVERT: A 133 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.3368 (p90) REVERT: A 309 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: A 314 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: A 346 ARG cc_start: 0.4733 (OUTLIER) cc_final: 0.3825 (mtm-85) REVERT: A 408 ARG cc_start: 0.5394 (OUTLIER) cc_final: 0.4503 (tpm170) REVERT: A 492 LEU cc_start: 0.1533 (OUTLIER) cc_final: 0.1250 (mm) REVERT: A 574 ASP cc_start: 0.7679 (m-30) cc_final: 0.7373 (m-30) REVERT: A 619 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 675 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6705 (mt0) REVERT: A 814 LYS cc_start: 0.8521 (mptt) cc_final: 0.7980 (mtpt) REVERT: A 947 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7210 (mtmt) REVERT: A 1031 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: A 1101 HIS cc_start: 0.7772 (m90) cc_final: 0.7400 (m90) REVERT: C 41 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8423 (mtpt) REVERT: C 133 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.5498 (p90) REVERT: C 211 ASN cc_start: 0.6876 (OUTLIER) cc_final: 0.6655 (p0) REVERT: C 347 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7001 (t80) REVERT: C 409 GLN cc_start: 0.8210 (mp-120) cc_final: 0.7757 (mm-40) REVERT: C 448 ASN cc_start: 0.7293 (m110) cc_final: 0.6956 (m-40) REVERT: C 453 TYR cc_start: 0.7620 (p90) cc_final: 0.6592 (p90) REVERT: C 493 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: C 516 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: C 675 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: C 854 LYS cc_start: 0.7945 (mttp) cc_final: 0.7633 (mtmm) REVERT: C 1031 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: B 96 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6082 (pp20) REVERT: B 99 ASN cc_start: 0.6694 (m-40) cc_final: 0.6075 (t0) REVERT: B 187 LYS cc_start: 0.5202 (OUTLIER) cc_final: 0.4546 (tppt) REVERT: B 215 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6874 (p0) REVERT: B 360 ASN cc_start: 0.7741 (t0) cc_final: 0.7359 (m-40) REVERT: B 420 ASP cc_start: 0.7767 (m-30) cc_final: 0.7469 (m-30) REVERT: B 456 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6811 (p90) REVERT: B 633 TRP cc_start: 0.8951 (OUTLIER) cc_final: 0.8509 (m100) REVERT: B 747 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7851 (m) REVERT: B 751 ASN cc_start: 0.8559 (m-40) cc_final: 0.8239 (m-40) REVERT: B 774 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7787 (mp-120) REVERT: B 811 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6992 (ptpp) REVERT: B 868 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 955 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7200 (m-40) REVERT: B 988 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7979 (mp0) outliers start: 164 outliers final: 97 residues processed: 355 average time/residue: 0.1572 time to fit residues: 91.0562 Evaluate side-chains 333 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 207 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 144 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 254 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 175 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 907 ASN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.186084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132357 restraints weight = 28897.142| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.08 r_work: 0.3101 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26074 Z= 0.168 Angle : 0.623 15.157 35639 Z= 0.301 Chirality : 0.047 0.386 4216 Planarity : 0.004 0.044 4497 Dihedral : 9.203 110.284 4877 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.72 % Favored : 92.93 % Rotamer: Outliers : 5.79 % Allowed : 25.30 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.15), residues: 3085 helix: 1.51 (0.21), residues: 686 sheet: -0.40 (0.20), residues: 610 loop : -1.82 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.027 0.001 TYR A 369 PHE 0.018 0.001 PHE C 168 TRP 0.012 0.001 TRP B 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00407 (25964) covalent geometry : angle 0.57658 (35351) SS BOND : bond 0.00516 ( 42) SS BOND : angle 1.18922 ( 84) hydrogen bonds : bond 0.04071 ( 916) hydrogen bonds : angle 5.40409 ( 2598) link_BETA1-3 : bond 0.00492 ( 1) link_BETA1-3 : angle 1.42493 ( 3) link_BETA1-4 : bond 0.00455 ( 27) link_BETA1-4 : angle 1.65474 ( 81) link_NAG-ASN : bond 0.00589 ( 40) link_NAG-ASN : angle 3.77979 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 217 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4817 (OUTLIER) cc_final: 0.4161 (t70) REVERT: A 97 LYS cc_start: 0.4406 (OUTLIER) cc_final: 0.3162 (mptt) REVERT: A 131 CYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5113 (m) REVERT: A 133 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.3343 (p90) REVERT: A 309 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: A 314 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8698 (tt0) REVERT: A 346 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.4248 (mtm-85) REVERT: A 408 ARG cc_start: 0.5639 (OUTLIER) cc_final: 0.4553 (tpm170) REVERT: A 464 PHE cc_start: 0.2117 (OUTLIER) cc_final: 0.1040 (t80) REVERT: A 492 LEU cc_start: 0.2054 (OUTLIER) cc_final: 0.1847 (mm) REVERT: A 574 ASP cc_start: 0.7788 (m-30) cc_final: 0.7447 (m-30) REVERT: A 619 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 675 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6670 (mt0) REVERT: A 814 LYS cc_start: 0.8607 (mptt) cc_final: 0.8011 (mtpt) REVERT: A 947 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7199 (mtmt) REVERT: A 1031 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: A 1101 HIS cc_start: 0.7906 (m90) cc_final: 0.7424 (m90) REVERT: C 41 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8393 (mtpt) REVERT: C 133 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5305 (p90) REVERT: C 135 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.3885 (m-80) REVERT: C 347 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7069 (t80) REVERT: C 409 GLN cc_start: 0.8170 (mp-120) cc_final: 0.7724 (mm-40) REVERT: C 448 ASN cc_start: 0.7139 (m110) cc_final: 0.6787 (m-40) REVERT: C 453 TYR cc_start: 0.7498 (p90) cc_final: 0.6447 (p90) REVERT: C 493 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6390 (tm-30) REVERT: C 516 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: C 675 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: C 1031 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: B 96 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: B 99 ASN cc_start: 0.6588 (m-40) cc_final: 0.6005 (t0) REVERT: B 187 LYS cc_start: 0.5105 (OUTLIER) cc_final: 0.4447 (tppt) REVERT: B 215 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6902 (p0) REVERT: B 226 LEU cc_start: 0.8462 (tp) cc_final: 0.8188 (mt) REVERT: B 360 ASN cc_start: 0.7766 (t0) cc_final: 0.7343 (m-40) REVERT: B 420 ASP cc_start: 0.7785 (m-30) cc_final: 0.7434 (m-30) REVERT: B 633 TRP cc_start: 0.8955 (OUTLIER) cc_final: 0.8495 (m100) REVERT: B 747 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7877 (m) REVERT: B 751 ASN cc_start: 0.8579 (m-40) cc_final: 0.8252 (m-40) REVERT: B 774 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7838 (mp-120) REVERT: B 811 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6887 (ptpp) REVERT: B 868 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: B 955 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7207 (m-40) REVERT: B 988 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8013 (mp0) outliers start: 158 outliers final: 107 residues processed: 351 average time/residue: 0.1605 time to fit residues: 91.8732 Evaluate side-chains 348 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 212 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 292 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 302 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.184620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131035 restraints weight = 42941.429| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.68 r_work: 0.3004 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26074 Z= 0.178 Angle : 0.629 15.214 35639 Z= 0.304 Chirality : 0.047 0.387 4216 Planarity : 0.004 0.044 4497 Dihedral : 9.165 110.116 4876 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.20 % Favored : 92.44 % Rotamer: Outliers : 5.86 % Allowed : 24.90 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.15), residues: 3085 helix: 1.49 (0.21), residues: 684 sheet: -0.42 (0.20), residues: 611 loop : -1.80 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.022 0.001 TYR C1067 PHE 0.023 0.001 PHE C 643 TRP 0.011 0.001 TRP B 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00434 (25964) covalent geometry : angle 0.58356 (35351) SS BOND : bond 0.00550 ( 42) SS BOND : angle 1.23322 ( 84) hydrogen bonds : bond 0.04144 ( 916) hydrogen bonds : angle 5.39185 ( 2598) link_BETA1-3 : bond 0.00492 ( 1) link_BETA1-3 : angle 1.42700 ( 3) link_BETA1-4 : bond 0.00458 ( 27) link_BETA1-4 : angle 1.65460 ( 81) link_NAG-ASN : bond 0.00580 ( 40) link_NAG-ASN : angle 3.78980 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 212 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5161 (OUTLIER) cc_final: 0.4418 (t70) REVERT: A 97 LYS cc_start: 0.4397 (OUTLIER) cc_final: 0.3105 (mptt) REVERT: A 131 CYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5271 (m) REVERT: A 133 PHE cc_start: 0.5671 (OUTLIER) cc_final: 0.3287 (p90) REVERT: A 281 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6620 (pt0) REVERT: A 309 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: A 314 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8702 (tt0) REVERT: A 346 ARG cc_start: 0.4557 (OUTLIER) cc_final: 0.3742 (mtm-85) REVERT: A 408 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.4560 (tpm170) REVERT: A 464 PHE cc_start: 0.1978 (OUTLIER) cc_final: 0.0860 (t80) REVERT: A 492 LEU cc_start: 0.1693 (OUTLIER) cc_final: 0.1437 (mm) REVERT: A 574 ASP cc_start: 0.7714 (m-30) cc_final: 0.7410 (m-30) REVERT: A 619 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 675 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6665 (mt0) REVERT: A 814 LYS cc_start: 0.8539 (mptt) cc_final: 0.8006 (mtpt) REVERT: A 947 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7215 (mtmt) REVERT: A 1031 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: A 1101 HIS cc_start: 0.7804 (m90) cc_final: 0.7298 (m170) REVERT: C 41 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8422 (mtpt) REVERT: C 133 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.5460 (p90) REVERT: C 135 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.4067 (m-80) REVERT: C 347 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7078 (t80) REVERT: C 409 GLN cc_start: 0.8220 (mp-120) cc_final: 0.7769 (mm-40) REVERT: C 448 ASN cc_start: 0.7242 (m110) cc_final: 0.6908 (m-40) REVERT: C 453 TYR cc_start: 0.7658 (p90) cc_final: 0.6649 (p90) REVERT: C 493 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: C 516 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: C 675 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: C 1031 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: B 96 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5990 (pp20) REVERT: B 99 ASN cc_start: 0.6645 (m-40) cc_final: 0.6087 (t0) REVERT: B 187 LYS cc_start: 0.5198 (OUTLIER) cc_final: 0.4536 (tppt) REVERT: B 360 ASN cc_start: 0.7790 (t0) cc_final: 0.7367 (m-40) REVERT: B 420 ASP cc_start: 0.7823 (m-30) cc_final: 0.7516 (m-30) REVERT: B 456 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6807 (p90) REVERT: B 633 TRP cc_start: 0.8955 (OUTLIER) cc_final: 0.8509 (m100) REVERT: B 747 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7915 (m) REVERT: B 751 ASN cc_start: 0.8574 (m-40) cc_final: 0.8251 (m-40) REVERT: B 774 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7781 (mp-120) REVERT: B 811 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6957 (ptpp) REVERT: B 868 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: B 955 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7214 (m-40) REVERT: B 988 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7990 (mp0) outliers start: 160 outliers final: 110 residues processed: 347 average time/residue: 0.1425 time to fit residues: 81.2240 Evaluate side-chains 351 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 211 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 167 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 163 optimal weight: 0.0570 chunk 172 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.188142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135185 restraints weight = 41850.618| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.57 r_work: 0.3009 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26074 Z= 0.114 Angle : 0.587 14.963 35639 Z= 0.282 Chirality : 0.046 0.388 4216 Planarity : 0.004 0.044 4497 Dihedral : 8.924 109.311 4876 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.52 % Favored : 93.12 % Rotamer: Outliers : 4.73 % Allowed : 26.06 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.15), residues: 3085 helix: 1.87 (0.21), residues: 677 sheet: -0.31 (0.20), residues: 612 loop : -1.72 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.020 0.001 TYR C1067 PHE 0.024 0.001 PHE C 643 TRP 0.009 0.001 TRP B 886 HIS 0.006 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00261 (25964) covalent geometry : angle 0.54245 (35351) SS BOND : bond 0.00380 ( 42) SS BOND : angle 0.97590 ( 84) hydrogen bonds : bond 0.03500 ( 916) hydrogen bonds : angle 5.17132 ( 2598) link_BETA1-3 : bond 0.00512 ( 1) link_BETA1-3 : angle 1.41847 ( 3) link_BETA1-4 : bond 0.00453 ( 27) link_BETA1-4 : angle 1.61123 ( 81) link_NAG-ASN : bond 0.00621 ( 40) link_NAG-ASN : angle 3.61317 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 228 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5017 (OUTLIER) cc_final: 0.4326 (t70) REVERT: A 97 LYS cc_start: 0.4263 (OUTLIER) cc_final: 0.3056 (mptt) REVERT: A 131 CYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5210 (m) REVERT: A 133 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.3355 (p90) REVERT: A 314 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: A 346 ARG cc_start: 0.4611 (OUTLIER) cc_final: 0.3827 (mtm-85) REVERT: A 408 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.4568 (tpm170) REVERT: A 492 LEU cc_start: 0.1683 (OUTLIER) cc_final: 0.1458 (mm) REVERT: A 574 ASP cc_start: 0.7702 (m-30) cc_final: 0.7399 (m-30) REVERT: A 619 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 675 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6705 (mt0) REVERT: A 814 LYS cc_start: 0.8522 (mptt) cc_final: 0.7962 (mtpp) REVERT: A 947 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7042 (mtmt) REVERT: A 1031 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: A 1101 HIS cc_start: 0.7760 (m90) cc_final: 0.7397 (m90) REVERT: C 41 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8400 (mtpt) REVERT: C 133 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.5380 (p90) REVERT: C 135 PHE cc_start: 0.6332 (OUTLIER) cc_final: 0.3954 (m-80) REVERT: C 169 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7167 (mt-10) REVERT: C 347 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7143 (t80) REVERT: C 409 GLN cc_start: 0.8207 (mp-120) cc_final: 0.7798 (mm-40) REVERT: C 448 ASN cc_start: 0.7128 (m110) cc_final: 0.6818 (m110) REVERT: C 493 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: C 516 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6672 (mm-30) REVERT: C 1031 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: B 79 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5679 (m-80) REVERT: B 96 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5962 (pp20) REVERT: B 99 ASN cc_start: 0.6479 (m-40) cc_final: 0.6025 (t0) REVERT: B 118 LEU cc_start: 0.8723 (tt) cc_final: 0.8518 (tt) REVERT: B 187 LYS cc_start: 0.5122 (OUTLIER) cc_final: 0.4475 (tppt) REVERT: B 360 ASN cc_start: 0.7739 (t0) cc_final: 0.7365 (m-40) REVERT: B 409 GLN cc_start: 0.8268 (mt0) cc_final: 0.7561 (mt0) REVERT: B 420 ASP cc_start: 0.7751 (m-30) cc_final: 0.7384 (m-30) REVERT: B 633 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.8475 (m100) REVERT: B 747 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7876 (m) REVERT: B 751 ASN cc_start: 0.8492 (m-40) cc_final: 0.8203 (m-40) REVERT: B 774 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7658 (mp-120) REVERT: B 811 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6943 (ptpp) REVERT: B 868 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: B 988 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7958 (mp0) outliers start: 129 outliers final: 86 residues processed: 333 average time/residue: 0.1465 time to fit residues: 78.9432 Evaluate side-chains 328 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 217 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 139 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 901 GLN A 907 ASN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 901 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN B1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.184533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128899 restraints weight = 41944.579| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.64 r_work: 0.2880 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26074 Z= 0.171 Angle : 0.636 15.102 35639 Z= 0.307 Chirality : 0.047 0.389 4216 Planarity : 0.004 0.043 4497 Dihedral : 8.939 109.603 4871 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.94 % Favored : 92.70 % Rotamer: Outliers : 4.99 % Allowed : 25.85 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 3085 helix: 1.68 (0.21), residues: 680 sheet: -0.33 (0.20), residues: 609 loop : -1.74 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.022 0.001 TYR C1067 PHE 0.024 0.001 PHE C 643 TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00417 (25964) covalent geometry : angle 0.58900 (35351) SS BOND : bond 0.00536 ( 42) SS BOND : angle 1.89118 ( 84) hydrogen bonds : bond 0.04054 ( 916) hydrogen bonds : angle 5.32821 ( 2598) link_BETA1-3 : bond 0.00499 ( 1) link_BETA1-3 : angle 1.44731 ( 3) link_BETA1-4 : bond 0.00467 ( 27) link_BETA1-4 : angle 1.62417 ( 81) link_NAG-ASN : bond 0.00573 ( 40) link_NAG-ASN : angle 3.69775 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 215 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4588 (OUTLIER) cc_final: 0.3979 (t70) REVERT: A 97 LYS cc_start: 0.4191 (OUTLIER) cc_final: 0.3062 (mptt) REVERT: A 131 CYS cc_start: 0.5863 (OUTLIER) cc_final: 0.4895 (m) REVERT: A 133 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.3387 (p90) REVERT: A 190 ARG cc_start: 0.7095 (mpt-90) cc_final: 0.6288 (mtm180) REVERT: A 281 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: A 314 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: A 346 ARG cc_start: 0.4786 (OUTLIER) cc_final: 0.4177 (mtm-85) REVERT: A 408 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.4472 (tpm170) REVERT: A 574 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: A 619 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 675 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6570 (mt0) REVERT: A 814 LYS cc_start: 0.8516 (mptt) cc_final: 0.7860 (mtpt) REVERT: A 947 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7049 (mtmt) REVERT: A 1031 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: A 1101 HIS cc_start: 0.7691 (m90) cc_final: 0.7131 (m90) REVERT: C 41 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7941 (mtpt) REVERT: C 133 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.5146 (p90) REVERT: C 135 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.4015 (m-80) REVERT: C 169 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7008 (mt-10) REVERT: C 347 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6995 (t80) REVERT: C 409 GLN cc_start: 0.8072 (mp-120) cc_final: 0.7653 (mm-40) REVERT: C 448 ASN cc_start: 0.6894 (m110) cc_final: 0.6557 (m-40) REVERT: C 493 GLN cc_start: 0.6486 (OUTLIER) cc_final: 0.6128 (tm-30) REVERT: C 516 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6528 (mm-30) REVERT: C 1031 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: B 79 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5670 (m-80) REVERT: B 96 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.5919 (pp20) REVERT: B 99 ASN cc_start: 0.6416 (m-40) cc_final: 0.5770 (t0) REVERT: B 187 LYS cc_start: 0.4996 (OUTLIER) cc_final: 0.4341 (tppt) REVERT: B 360 ASN cc_start: 0.7775 (t0) cc_final: 0.7314 (m-40) REVERT: B 420 ASP cc_start: 0.7589 (m-30) cc_final: 0.7176 (m-30) REVERT: B 633 TRP cc_start: 0.8853 (OUTLIER) cc_final: 0.8338 (m100) REVERT: B 661 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8232 (tt0) REVERT: B 747 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7679 (m) REVERT: B 751 ASN cc_start: 0.8394 (m-40) cc_final: 0.8076 (m-40) REVERT: B 774 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7669 (mp-120) REVERT: B 811 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6719 (ptpp) REVERT: B 868 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: B 955 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.6897 (m-40) REVERT: B 988 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7693 (mp0) outliers start: 136 outliers final: 98 residues processed: 328 average time/residue: 0.1524 time to fit residues: 80.8901 Evaluate side-chains 339 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 214 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 243 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 186 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 199 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 907 ASN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.184147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130420 restraints weight = 39352.902| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.63 r_work: 0.2940 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 26074 Z= 0.150 Angle : 0.619 15.186 35639 Z= 0.299 Chirality : 0.047 0.389 4216 Planarity : 0.004 0.042 4497 Dihedral : 8.875 109.476 4871 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.65 % Favored : 92.99 % Rotamer: Outliers : 5.10 % Allowed : 25.85 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3085 helix: 1.77 (0.21), residues: 674 sheet: -0.29 (0.20), residues: 619 loop : -1.73 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.021 0.001 TYR C1067 PHE 0.023 0.001 PHE C 643 TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00362 (25964) covalent geometry : angle 0.57208 (35351) SS BOND : bond 0.00493 ( 42) SS BOND : angle 1.79439 ( 84) hydrogen bonds : bond 0.03845 ( 916) hydrogen bonds : angle 5.28137 ( 2598) link_BETA1-3 : bond 0.00499 ( 1) link_BETA1-3 : angle 1.43533 ( 3) link_BETA1-4 : bond 0.00457 ( 27) link_BETA1-4 : angle 1.61412 ( 81) link_NAG-ASN : bond 0.00589 ( 40) link_NAG-ASN : angle 3.66774 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 221 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4879 (OUTLIER) cc_final: 0.4199 (t70) REVERT: A 97 LYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3047 (mptt) REVERT: A 131 CYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5063 (m) REVERT: A 133 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.3330 (p90) REVERT: A 190 ARG cc_start: 0.7237 (mpt-90) cc_final: 0.6476 (mtm180) REVERT: A 281 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6525 (pt0) REVERT: A 314 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: A 346 ARG cc_start: 0.4596 (OUTLIER) cc_final: 0.3984 (mtm-85) REVERT: A 408 ARG cc_start: 0.5278 (OUTLIER) cc_final: 0.4569 (tpm170) REVERT: A 464 PHE cc_start: 0.1865 (OUTLIER) cc_final: 0.0790 (t80) REVERT: A 574 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: A 619 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 675 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6785 (mt0) REVERT: A 814 LYS cc_start: 0.8532 (mptt) cc_final: 0.7949 (mtpt) REVERT: A 947 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7116 (mtmt) REVERT: A 1031 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: A 1101 HIS cc_start: 0.7770 (m90) cc_final: 0.7287 (m90) REVERT: C 41 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8296 (mtpt) REVERT: C 133 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.5276 (p90) REVERT: C 135 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.3967 (m-80) REVERT: C 169 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 347 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7129 (t80) REVERT: C 409 GLN cc_start: 0.8170 (mp-120) cc_final: 0.7762 (mm-40) REVERT: C 448 ASN cc_start: 0.7071 (m110) cc_final: 0.6725 (m-40) REVERT: C 493 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: C 516 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6594 (mm-30) REVERT: C 1031 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: B 79 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: B 96 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5912 (pp20) REVERT: B 99 ASN cc_start: 0.6404 (m-40) cc_final: 0.5948 (t0) REVERT: B 187 LYS cc_start: 0.5137 (OUTLIER) cc_final: 0.4472 (tppt) REVERT: B 360 ASN cc_start: 0.7779 (t0) cc_final: 0.7347 (m-40) REVERT: B 420 ASP cc_start: 0.7710 (m-30) cc_final: 0.7334 (m-30) REVERT: B 633 TRP cc_start: 0.8919 (OUTLIER) cc_final: 0.8441 (m100) REVERT: B 661 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8358 (tt0) REVERT: B 747 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 751 ASN cc_start: 0.8478 (m-40) cc_final: 0.8171 (m-40) REVERT: B 774 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7735 (mp-120) REVERT: B 811 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6849 (ptpp) REVERT: B 868 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 955 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7075 (m-40) REVERT: B 988 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7839 (mp0) outliers start: 139 outliers final: 101 residues processed: 336 average time/residue: 0.1652 time to fit residues: 90.2906 Evaluate side-chains 349 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 220 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 134 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 267 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 907 ASN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 901 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN B1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.185958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128321 restraints weight = 46185.542| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.75 r_work: 0.2900 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26074 Z= 0.126 Angle : 0.603 15.150 35639 Z= 0.291 Chirality : 0.046 0.389 4216 Planarity : 0.004 0.041 4497 Dihedral : 8.790 109.388 4871 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.59 % Favored : 93.06 % Rotamer: Outliers : 4.84 % Allowed : 25.88 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3085 helix: 1.93 (0.21), residues: 668 sheet: -0.27 (0.20), residues: 609 loop : -1.65 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.020 0.001 TYR C1067 PHE 0.023 0.001 PHE C 643 TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00295 (25964) covalent geometry : angle 0.55718 (35351) SS BOND : bond 0.00417 ( 42) SS BOND : angle 1.58085 ( 84) hydrogen bonds : bond 0.03641 ( 916) hydrogen bonds : angle 5.21571 ( 2598) link_BETA1-3 : bond 0.00499 ( 1) link_BETA1-3 : angle 1.43834 ( 3) link_BETA1-4 : bond 0.00457 ( 27) link_BETA1-4 : angle 1.60324 ( 81) link_NAG-ASN : bond 0.00604 ( 40) link_NAG-ASN : angle 3.61394 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 218 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4597 (OUTLIER) cc_final: 0.3976 (t70) REVERT: A 97 LYS cc_start: 0.4292 (OUTLIER) cc_final: 0.3231 (mptt) REVERT: A 131 CYS cc_start: 0.5818 (OUTLIER) cc_final: 0.4832 (m) REVERT: A 133 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.3412 (p90) REVERT: A 190 ARG cc_start: 0.7113 (mpt-90) cc_final: 0.6312 (mtm180) REVERT: A 281 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6384 (pt0) REVERT: A 314 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: A 346 ARG cc_start: 0.4745 (OUTLIER) cc_final: 0.4231 (mtm-85) REVERT: A 408 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4561 (tpm170) REVERT: A 574 ASP cc_start: 0.7358 (m-30) cc_final: 0.6969 (m-30) REVERT: A 619 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 675 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6748 (mt0) REVERT: A 814 LYS cc_start: 0.8531 (mptt) cc_final: 0.7871 (mtpt) REVERT: A 947 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.6949 (mtmt) REVERT: A 1031 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: A 1101 HIS cc_start: 0.7695 (m90) cc_final: 0.7154 (m90) REVERT: C 41 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8105 (mtpt) REVERT: C 133 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.5051 (p90) REVERT: C 135 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.3919 (m-80) REVERT: C 169 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7035 (mt-10) REVERT: C 347 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7068 (t80) REVERT: C 409 GLN cc_start: 0.8085 (mp-120) cc_final: 0.7696 (mm-40) REVERT: C 448 ASN cc_start: 0.6860 (m110) cc_final: 0.6556 (m110) REVERT: C 493 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6154 (tm-30) REVERT: C 516 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: C 1031 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: B 79 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5673 (m-80) REVERT: B 96 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5903 (pp20) REVERT: B 99 ASN cc_start: 0.6418 (m-40) cc_final: 0.5853 (t0) REVERT: B 187 LYS cc_start: 0.5056 (OUTLIER) cc_final: 0.4363 (tppt) REVERT: B 360 ASN cc_start: 0.7778 (t0) cc_final: 0.7348 (m-40) REVERT: B 409 GLN cc_start: 0.7899 (mt0) cc_final: 0.7208 (mt0) REVERT: B 420 ASP cc_start: 0.7600 (m-30) cc_final: 0.7167 (m-30) REVERT: B 633 TRP cc_start: 0.8841 (OUTLIER) cc_final: 0.8317 (m100) REVERT: B 747 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7651 (m) REVERT: B 751 ASN cc_start: 0.8347 (m-40) cc_final: 0.8022 (m-40) REVERT: B 774 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7630 (mp-120) REVERT: B 811 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6641 (ptpp) REVERT: B 868 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 988 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7702 (mp0) outliers start: 132 outliers final: 100 residues processed: 326 average time/residue: 0.1700 time to fit residues: 89.7304 Evaluate side-chains 342 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 217 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 268 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 907 ASN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 901 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1010 GLN B1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.185597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130835 restraints weight = 44315.538| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.67 r_work: 0.2952 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 26074 Z= 0.138 Angle : 0.607 15.125 35639 Z= 0.292 Chirality : 0.046 0.390 4216 Planarity : 0.004 0.041 4497 Dihedral : 8.706 109.173 4869 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.85 % Favored : 92.80 % Rotamer: Outliers : 4.91 % Allowed : 25.85 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 3085 helix: 1.85 (0.21), residues: 674 sheet: -0.26 (0.20), residues: 609 loop : -1.67 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.021 0.001 TYR C1067 PHE 0.022 0.001 PHE C 643 TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00331 (25964) covalent geometry : angle 0.56076 (35351) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.58863 ( 84) hydrogen bonds : bond 0.03738 ( 916) hydrogen bonds : angle 5.20849 ( 2598) link_BETA1-3 : bond 0.00508 ( 1) link_BETA1-3 : angle 1.45054 ( 3) link_BETA1-4 : bond 0.00459 ( 27) link_BETA1-4 : angle 1.59286 ( 81) link_NAG-ASN : bond 0.00591 ( 40) link_NAG-ASN : angle 3.61907 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7031.19 seconds wall clock time: 121 minutes 5.94 seconds (7265.94 seconds total)