Starting phenix.real_space_refine on Tue Aug 26 13:11:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxd_64581/08_2025/9uxd_64581.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxd_64581/08_2025/9uxd_64581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxd_64581/08_2025/9uxd_64581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxd_64581/08_2025/9uxd_64581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxd_64581/08_2025/9uxd_64581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxd_64581/08_2025/9uxd_64581.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 152 5.16 5 C 22708 2.51 5 N 5919 2.21 5 O 7060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35839 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8315 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 58, 'TRANS': 1003} Chain breaks: 5 Chain: "B" Number of atoms: 8279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8279 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 58, 'TRANS': 999} Chain breaks: 5 Chain: "C" Number of atoms: 8307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8307 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 5 Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain: "E" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1617 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain: "L" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1617 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "J" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain: "K" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1617 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.45, per 1000 atoms: 0.21 Number of scatterers: 35839 At special positions: 0 Unit cell: (161.71, 147.29, 234.84, 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 152 16.00 O 7060 8.00 N 5919 7.00 C 22708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " 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=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG I 1 " - " FUC I 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 4 " " NAG V 1 " - " FUC V 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 125 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG F 1 " - " ASN C 234 " " NAG G 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 343 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 717 " " NAG S 1 " - " ASN A 801 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8372 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 78 sheets defined 18.2% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.663A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.342A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.695A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.857A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.623A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.589A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.052A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.233A 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 945 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 1033 removed outlier: 4.942A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.900A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.326A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.371A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.507A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.980A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.206A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.972A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.399A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.725A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.460A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.030A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.656A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.536A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.076A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.529A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.535A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 1032 removed outlier: 4.876A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'E' and resid 118 through 124 removed outlier: 3.704A pdb=" N SER E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 removed outlier: 3.715A pdb=" N LYS E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS E 186 " --> pdb=" O ASP E 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.717A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'L' and resid 120 through 125 removed outlier: 4.351A pdb=" N GLY L 125 " --> pdb=" O GLN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 184 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'K' and resid 118 through 124 removed outlier: 3.583A pdb=" N SER K 124 " --> pdb=" O GLU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 186 removed outlier: 3.511A pdb=" N LYS K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS K 186 " --> pdb=" O ASP K 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.679A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.309A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.968A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.146A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.995A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.518A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.930A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.307A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.975A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.111A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.768A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.314A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.777A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.822A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.669A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 157 removed outlier: 6.281A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.882A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.012A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.022A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.074A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.664A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.414A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.578A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.912A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.074A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.060A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.181A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.000A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.980A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.582A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.706A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.639A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.607A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.625A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.565A pdb=" N ALA D 92 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 133 through 137 Processing sheet with id=AF7, first strand: chain 'D' and resid 164 through 167 removed outlier: 3.714A pdb=" N THR D 164 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 220 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 182 through 184 removed outlier: 3.719A pdb=" N LEU D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.652A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 75 " --> pdb=" O SER E 64 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.678A pdb=" N LEU E 11 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 111 through 115 removed outlier: 6.309A pdb=" N TYR E 170 " --> pdb=" O ASN E 135 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 150 through 151 removed outlier: 3.606A pdb=" N LYS E 142 " --> pdb=" O THR E 194 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR E 189 " --> pdb=" O PHE E 206 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.976A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.702A pdb=" N MET H 34 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 133 through 137 removed outlier: 3.982A pdb=" N PHE H 135 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU H 154 " --> pdb=" O PHE H 135 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 164 through 167 removed outlier: 3.671A pdb=" N THR H 164 " --> pdb=" O ASN H 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL H 220 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 182 through 183 removed outlier: 3.677A pdb=" N SER H 190 " --> pdb=" O VAL H 182 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.579A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.472A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.844A pdb=" N LEU L 91 " --> pdb=" O SER L 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 111 through 115 removed outlier: 3.615A pdb=" N ASN L 135 " --> pdb=" O TYR L 170 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR L 170 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 151 through 152 removed outlier: 3.605A pdb=" N GLN L 152 " --> pdb=" O TRP L 145 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP L 145 " --> pdb=" O GLN L 152 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.820A pdb=" N TRP J 33 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.237A pdb=" N CYS J 96 " --> pdb=" O TRP J 116 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP J 116 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG J 98 " --> pdb=" O ASP J 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP J 114 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR J 112 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 133 through 137 removed outlier: 3.652A pdb=" N PHE J 135 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU J 154 " --> pdb=" O PHE J 135 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.602A pdb=" N THR J 164 " --> pdb=" O ASN J 212 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR J 207 " --> pdb=" O VAL J 224 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 182 through 184 removed outlier: 3.806A pdb=" N LEU J 188 " --> pdb=" O GLN J 184 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 5 through 7 removed outlier: 4.040A pdb=" N SER K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 19 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER K 68 " --> pdb=" O ASP K 71 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR K 73 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.576A pdb=" N ALA K 35 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AI5, first strand: chain 'K' and resid 111 through 115 removed outlier: 6.390A pdb=" N TYR K 170 " --> pdb=" O ASN K 135 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 150 through 152 removed outlier: 4.037A pdb=" N TRP K 145 " --> pdb=" O GLN K 152 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN K 144 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU K 192 " --> pdb=" O GLN K 144 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL K 193 " --> pdb=" O VAL K 202 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL K 202 " --> pdb=" O VAL K 193 " (cutoff:3.500A) 1364 hydrogen bonds defined for protein. 3684 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: 7.87 Time building geometry restraints manager: 3.45 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: 11353 1.34 - 1.47: 9200 1.47 - 1.59: 15915 1.59 - 1.71: 0 1.71 - 1.84: 193 Bond restraints: 36661 Sorted by residual: bond pdb=" N ILE D 107 " pdb=" CA ILE D 107 " ideal model delta sigma weight residual 1.462 1.498 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" N ILE D 106 " pdb=" CA ILE D 106 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.64e+00 bond pdb=" N VAL A 511 " pdb=" CA VAL A 511 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.81e+00 bond pdb=" N ILE A 434 " pdb=" CA ILE A 434 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.80e+00 bond pdb=" N VAL A 341 " pdb=" CA VAL A 341 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.69e+00 ... (remaining 36656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 49301 2.88 - 5.76: 513 5.76 - 8.64: 63 8.64 - 11.52: 13 11.52 - 14.40: 5 Bond angle restraints: 49895 Sorted by residual: angle pdb=" CB MET E 4 " pdb=" CG MET E 4 " pdb=" SD MET E 4 " ideal model delta sigma weight residual 112.70 127.10 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" CA ASN B 657 " pdb=" CB ASN B 657 " pdb=" CG ASN B 657 " ideal model delta sigma weight residual 112.60 117.14 -4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 126.15 -13.45 3.00e+00 1.11e-01 2.01e+01 angle pdb=" N ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 110.39 117.67 -7.28 1.66e+00 3.63e-01 1.92e+01 angle pdb=" C ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 110.31 101.30 9.01 2.09e+00 2.29e-01 1.86e+01 ... (remaining 49890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.70: 20960 18.70 - 37.40: 1379 37.40 - 56.10: 313 56.10 - 74.80: 61 74.80 - 93.50: 30 Dihedral angle restraints: 22743 sinusoidal: 9711 harmonic: 13032 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 159.98 -66.98 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CA THR C 602 " pdb=" C THR C 602 " pdb=" N ASN C 603 " pdb=" CA ASN C 603 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA CYS C 760 " pdb=" C CYS C 760 " pdb=" N THR C 761 " pdb=" CA THR C 761 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 22740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 5796 0.170 - 0.341: 26 0.341 - 0.511: 2 0.511 - 0.682: 0 0.682 - 0.852: 1 Chirality restraints: 5825 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.49e+01 chirality pdb=" C1 FUC P 4 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 4 " pdb=" O5 FUC P 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.63e+01 ... (remaining 5822 not shown) Planarity restraints: 6410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " -0.061 2.00e-02 2.50e+03 5.01e-02 3.14e+01 pdb=" C7 NAG P 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " 0.080 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.502 9.50e-02 1.11e+02 2.25e-01 3.10e+01 pdb=" NE ARG A 346 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.060 2.00e-02 2.50e+03 4.97e-02 3.08e+01 pdb=" C7 NAG P 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.079 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.010 2.00e-02 2.50e+03 ... (remaining 6407 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 15264 2.92 - 3.42: 33457 3.42 - 3.91: 59171 3.91 - 4.41: 65510 4.41 - 4.90: 111403 Nonbonded interactions: 284805 Sorted by model distance: nonbonded pdb=" O ASN B 360 " pdb=" OD1 ASN B 360 " model vdw 2.425 3.040 nonbonded pdb=" O THR A 345 " pdb=" NH2 ARG A 509 " model vdw 2.464 3.120 nonbonded pdb=" O5 NAG B1306 " pdb=" O6 NAG B1306 " model vdw 2.467 2.432 nonbonded pdb=" O5 NAG R 1 " pdb=" O6 NAG R 1 " model vdw 2.469 2.432 nonbonded pdb=" ND2 ASN B 657 " pdb=" N2 NAG B1307 " model vdw 2.483 2.560 ... (remaining 284800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 176 or resid 186 through 827 or resid 855 throu \ gh 1308)) selection = (chain 'B' and (resid 14 through 621 or resid 641 through 827 or resid 855 throu \ gh 1308)) selection = (chain 'C' and (resid 14 through 176 or resid 186 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.030 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 0.065 36773 Z= 0.171 Angle : 0.795 19.375 50183 Z= 0.388 Chirality : 0.051 0.852 5825 Planarity : 0.006 0.225 6368 Dihedral : 13.292 93.501 14236 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.28 % Allowed : 16.48 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.11 (0.13), residues: 4447 helix: 2.07 (0.20), residues: 704 sheet: 0.41 (0.14), residues: 1297 loop : -1.02 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 55 TYR 0.032 0.001 TYR C 453 PHE 0.031 0.002 PHE B 133 TRP 0.045 0.002 TRP K 36 HIS 0.016 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00333 (36661) covalent geometry : angle 0.73085 (49895) SS BOND : bond 0.00508 ( 45) SS BOND : angle 1.29408 ( 90) hydrogen bonds : bond 0.12348 ( 1342) hydrogen bonds : angle 7.59245 ( 3684) Misc. bond : bond 0.00318 ( 1) link_BETA1-4 : bond 0.01497 ( 21) link_BETA1-4 : angle 2.43631 ( 63) link_BETA1-6 : bond 0.01467 ( 3) link_BETA1-6 : angle 3.23379 ( 9) link_NAG-ASN : bond 0.00943 ( 42) link_NAG-ASN : angle 5.93523 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 433 time to evaluate : 0.943 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 88 ASP cc_start: 0.7582 (m-30) cc_final: 0.7005 (p0) REVERT: A 237 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7353 (mtp85) REVERT: A 298 GLU cc_start: 0.8781 (tt0) cc_final: 0.8198 (mt-10) REVERT: A 368 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 371 SER cc_start: 0.8535 (t) cc_final: 0.8217 (p) REVERT: A 420 ASP cc_start: 0.8828 (m-30) cc_final: 0.8520 (m-30) REVERT: A 428 ASP cc_start: 0.9174 (p0) cc_final: 0.8940 (p0) REVERT: A 465 GLU cc_start: 0.9102 (tt0) cc_final: 0.8722 (tt0) REVERT: A 471 GLU cc_start: 0.8510 (tp30) cc_final: 0.8251 (mt-10) REVERT: A 571 ASP cc_start: 0.8428 (t70) cc_final: 0.8074 (t0) REVERT: A 697 MET cc_start: 0.9087 (ptm) cc_final: 0.8743 (ptm) REVERT: B 52 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7777 (tm-30) REVERT: B 190 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7690 (mtt90) REVERT: B 207 HIS cc_start: 0.7928 (t-170) cc_final: 0.7683 (t70) REVERT: B 239 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7514 (mm-40) REVERT: B 319 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7863 (tpt170) REVERT: B 378 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8744 (ptmm) REVERT: B 489 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: B 529 LYS cc_start: 0.8552 (mttm) cc_final: 0.8341 (mmtp) REVERT: B 586 ASP cc_start: 0.8799 (m-30) cc_final: 0.8362 (m-30) REVERT: B 587 ILE cc_start: 0.9279 (mt) cc_final: 0.9070 (mp) REVERT: B 605 SER cc_start: 0.9076 (t) cc_final: 0.8526 (m) REVERT: B 773 GLU cc_start: 0.8392 (tt0) cc_final: 0.8159 (tt0) REVERT: C 81 ASN cc_start: 0.8567 (p0) cc_final: 0.8123 (p0) REVERT: C 177 MET cc_start: -0.3340 (mmt) cc_final: -0.4710 (mpp) REVERT: C 190 ARG cc_start: 0.7312 (mmm160) cc_final: 0.6716 (mmt90) REVERT: C 197 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8531 (pp) REVERT: C 202 LYS cc_start: 0.8722 (mttt) cc_final: 0.8026 (mtmm) REVERT: C 304 LYS cc_start: 0.9275 (mttt) cc_final: 0.9023 (mmmt) REVERT: C 353 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.5531 (p-90) REVERT: C 821 LEU cc_start: 0.8817 (tp) cc_final: 0.8526 (mp) REVERT: C 988 GLU cc_start: 0.8705 (tp30) cc_final: 0.8461 (tp30) REVERT: D 13 GLN cc_start: 0.8399 (pm20) cc_final: 0.8093 (pp30) REVERT: H 179 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.4619 (t80) REVERT: H 207 TYR cc_start: 0.2060 (t80) cc_final: 0.0980 (m-10) REVERT: J 36 TRP cc_start: 0.6743 (t-100) cc_final: 0.6221 (t-100) REVERT: J 52 ASN cc_start: 0.6470 (p0) cc_final: 0.6222 (p0) REVERT: J 124 VAL cc_start: 0.5273 (OUTLIER) cc_final: 0.4955 (p) REVERT: K 76 ILE cc_start: 0.6802 (mm) cc_final: 0.6597 (mt) outliers start: 50 outliers final: 28 residues processed: 468 average time/residue: 0.2131 time to fit residues: 159.9596 Evaluate side-chains 406 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 179 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 91 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 30.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 245 HIS A 271 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 519 HIS A 658 ASN A 955 ASN A1135 ASN B 69 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 498 GLN C 146 HIS C 207 HIS C 239 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 519 HIS C 762 GLN C 804 GLN C1002 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN H 39 GLN H 82 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 144 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN J 177 HIS J 184 GLN J 213 HIS K 135 ASN K 152 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.153192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088410 restraints weight = 66706.572| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.93 r_work: 0.3038 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 36773 Z= 0.300 Angle : 0.756 20.262 50183 Z= 0.370 Chirality : 0.049 0.240 5825 Planarity : 0.005 0.062 6368 Dihedral : 7.134 99.950 6315 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.71 % Allowed : 14.11 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.27 (0.12), residues: 4447 helix: 1.81 (0.20), residues: 722 sheet: 0.28 (0.14), residues: 1318 loop : -1.08 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.024 0.002 TYR L 92 PHE 0.039 0.002 PHE L 72 TRP 0.022 0.002 TRP L 145 HIS 0.014 0.002 HIS L 186 Details of bonding type rmsd covalent geometry : bond 0.00713 (36661) covalent geometry : angle 0.71519 (49895) SS BOND : bond 0.00482 ( 45) SS BOND : angle 1.82912 ( 90) hydrogen bonds : bond 0.05592 ( 1342) hydrogen bonds : angle 6.43857 ( 3684) Misc. bond : bond 0.00295 ( 1) link_BETA1-4 : bond 0.00317 ( 21) link_BETA1-4 : angle 2.06183 ( 63) link_BETA1-6 : bond 0.00209 ( 3) link_BETA1-6 : angle 2.12451 ( 9) link_NAG-ASN : bond 0.00742 ( 42) link_NAG-ASN : angle 4.48876 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 387 time to evaluate : 1.366 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7904 (m-30) cc_final: 0.7656 (m-30) REVERT: A 220 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5668 (t80) REVERT: A 237 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7790 (mtp85) REVERT: A 298 GLU cc_start: 0.8991 (tt0) cc_final: 0.8423 (mt-10) REVERT: A 408 ARG cc_start: 0.8742 (ppt170) cc_final: 0.8506 (ppt170) REVERT: A 420 ASP cc_start: 0.9007 (m-30) cc_final: 0.8689 (m-30) REVERT: A 423 TYR cc_start: 0.8926 (t80) cc_final: 0.8592 (t80) REVERT: A 428 ASP cc_start: 0.9174 (p0) cc_final: 0.8891 (p0) REVERT: A 465 GLU cc_start: 0.9090 (tt0) cc_final: 0.8838 (tt0) REVERT: A 471 GLU cc_start: 0.8720 (tp30) cc_final: 0.8390 (mt-10) REVERT: A 571 ASP cc_start: 0.8470 (t70) cc_final: 0.8091 (t0) REVERT: A 697 MET cc_start: 0.9169 (ptm) cc_final: 0.8851 (ptm) REVERT: A 988 GLU cc_start: 0.8498 (mp0) cc_final: 0.8292 (mp0) REVERT: B 52 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 190 ARG cc_start: 0.8257 (mtt90) cc_final: 0.7930 (mtt90) REVERT: B 239 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7413 (mm-40) REVERT: B 378 LYS cc_start: 0.9018 (ptpp) cc_final: 0.8803 (ptmm) REVERT: B 449 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 523 THR cc_start: 0.8844 (p) cc_final: 0.8376 (t) REVERT: B 529 LYS cc_start: 0.8745 (mttm) cc_final: 0.8533 (mmtp) REVERT: B 583 GLU cc_start: 0.8113 (tp30) cc_final: 0.7862 (tt0) REVERT: B 586 ASP cc_start: 0.8887 (m-30) cc_final: 0.8474 (m-30) REVERT: B 740 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8820 (ttt) REVERT: B 773 GLU cc_start: 0.8497 (tt0) cc_final: 0.8193 (tt0) REVERT: B 1142 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8260 (tm-30) REVERT: C 18 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5290 (tt) REVERT: C 81 ASN cc_start: 0.8827 (p0) cc_final: 0.8467 (p0) REVERT: C 140 PHE cc_start: 0.8925 (p90) cc_final: 0.8694 (p90) REVERT: C 177 MET cc_start: -0.2608 (mmt) cc_final: -0.4071 (mpp) REVERT: C 197 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8461 (pp) REVERT: C 202 LYS cc_start: 0.8985 (mttt) cc_final: 0.8441 (mttp) REVERT: C 353 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.6995 (p-90) REVERT: C 497 PHE cc_start: 0.4233 (OUTLIER) cc_final: 0.2924 (t80) REVERT: C 506 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6794 (mm110) REVERT: D 13 GLN cc_start: 0.8645 (pm20) cc_final: 0.8331 (pp30) REVERT: D 67 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6795 (mpp80) REVERT: D 74 ASN cc_start: 0.7424 (t0) cc_final: 0.7017 (m-40) REVERT: D 86 LEU cc_start: 0.8157 (tp) cc_final: 0.7692 (mp) REVERT: D 87 ARG cc_start: 0.7258 (mtm110) cc_final: 0.6858 (mtm110) REVERT: D 107 ILE cc_start: 0.7506 (mm) cc_final: 0.7122 (mm) REVERT: E 113 PHE cc_start: 0.6957 (m-80) cc_final: 0.6706 (m-80) REVERT: H 38 ARG cc_start: 0.8243 (ptp90) cc_final: 0.7996 (ptp90) REVERT: H 54 ASP cc_start: 0.8811 (m-30) cc_final: 0.8526 (p0) REVERT: H 67 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.5914 (ptm160) REVERT: H 179 PHE cc_start: 0.5166 (OUTLIER) cc_final: 0.4913 (t80) REVERT: H 207 TYR cc_start: 0.2494 (t80) cc_final: 0.1643 (m-10) REVERT: L 4 MET cc_start: 0.6936 (mmm) cc_final: 0.6469 (mmm) REVERT: L 24 ARG cc_start: 0.8059 (mpp80) cc_final: 0.7690 (mpp80) REVERT: L 36 TRP cc_start: 0.7100 (OUTLIER) cc_final: 0.6418 (m-90) REVERT: L 88 TYR cc_start: 0.7459 (m-80) cc_final: 0.7040 (m-10) REVERT: L 139 ARG cc_start: 0.6554 (mtt-85) cc_final: 0.5624 (mmp80) REVERT: J 35 HIS cc_start: 0.8237 (m170) cc_final: 0.7559 (m-70) REVERT: J 36 TRP cc_start: 0.7285 (t-100) cc_final: 0.6384 (t-100) REVERT: J 124 VAL cc_start: 0.6637 (OUTLIER) cc_final: 0.6087 (p) REVERT: K 87 TYR cc_start: 0.8128 (m-80) cc_final: 0.7857 (m-80) outliers start: 145 outliers final: 75 residues processed: 494 average time/residue: 0.2046 time to fit residues: 164.9415 Evaluate side-chains 439 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 350 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 PHE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 36 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 118 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 99 optimal weight: 0.9990 chunk 391 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 193 optimal weight: 0.6980 chunk 394 optimal weight: 10.0000 chunk 285 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B1135 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 762 GLN D 3 GLN D 39 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN K 135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.156701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092789 restraints weight = 66744.542| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.99 r_work: 0.3093 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36773 Z= 0.124 Angle : 0.624 20.326 50183 Z= 0.302 Chirality : 0.045 0.231 5825 Planarity : 0.004 0.067 6368 Dihedral : 6.472 96.233 6300 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.02 % Allowed : 15.33 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.13 (0.13), residues: 4447 helix: 2.07 (0.20), residues: 723 sheet: 0.26 (0.14), residues: 1336 loop : -0.98 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 139 TYR 0.019 0.001 TYR B1067 PHE 0.022 0.001 PHE L 72 TRP 0.014 0.001 TRP L 145 HIS 0.008 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00274 (36661) covalent geometry : angle 0.58594 (49895) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.42941 ( 90) hydrogen bonds : bond 0.04286 ( 1342) hydrogen bonds : angle 5.94633 ( 3684) Misc. bond : bond 0.00230 ( 1) link_BETA1-4 : bond 0.00466 ( 21) link_BETA1-4 : angle 1.51438 ( 63) link_BETA1-6 : bond 0.00233 ( 3) link_BETA1-6 : angle 1.78466 ( 9) link_NAG-ASN : bond 0.00552 ( 42) link_NAG-ASN : angle 4.02655 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 384 time to evaluate : 1.220 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7901 (m-30) cc_final: 0.7645 (m-30) REVERT: A 237 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7784 (mtp85) REVERT: A 298 GLU cc_start: 0.8983 (tt0) cc_final: 0.8396 (mt-10) REVERT: A 408 ARG cc_start: 0.8793 (ppt170) cc_final: 0.8501 (ppt170) REVERT: A 420 ASP cc_start: 0.8986 (m-30) cc_final: 0.8646 (m-30) REVERT: A 423 TYR cc_start: 0.8876 (t80) cc_final: 0.8665 (t80) REVERT: A 428 ASP cc_start: 0.9150 (p0) cc_final: 0.8900 (p0) REVERT: A 465 GLU cc_start: 0.9103 (tt0) cc_final: 0.8823 (tt0) REVERT: A 571 ASP cc_start: 0.8428 (t70) cc_final: 0.8054 (t0) REVERT: A 617 CYS cc_start: 0.6417 (OUTLIER) cc_final: 0.5786 (m) REVERT: A 697 MET cc_start: 0.9153 (ptm) cc_final: 0.8855 (ptm) REVERT: A 988 GLU cc_start: 0.8619 (mp0) cc_final: 0.8379 (mp0) REVERT: B 52 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 190 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7778 (mtt90) REVERT: B 204 TYR cc_start: 0.8724 (m-80) cc_final: 0.8114 (m-80) REVERT: B 239 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7440 (mm-40) REVERT: B 449 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: B 523 THR cc_start: 0.8707 (p) cc_final: 0.8294 (t) REVERT: B 529 LYS cc_start: 0.8718 (mttm) cc_final: 0.8497 (mmtp) REVERT: B 583 GLU cc_start: 0.7980 (tp30) cc_final: 0.7763 (tt0) REVERT: B 586 ASP cc_start: 0.8890 (m-30) cc_final: 0.8476 (m-30) REVERT: B 740 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8731 (ttt) REVERT: B 988 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: B 1142 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 18 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5381 (tt) REVERT: C 81 ASN cc_start: 0.8801 (p0) cc_final: 0.8463 (p0) REVERT: C 140 PHE cc_start: 0.8927 (p90) cc_final: 0.8572 (p90) REVERT: C 177 MET cc_start: -0.2705 (mmt) cc_final: -0.4429 (mpp) REVERT: C 197 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8558 (pp) REVERT: C 202 LYS cc_start: 0.8973 (mttt) cc_final: 0.8281 (mtmm) REVERT: C 353 TRP cc_start: 0.8045 (OUTLIER) cc_final: 0.7080 (p-90) REVERT: C 409 GLN cc_start: 0.8535 (mt0) cc_final: 0.8326 (mt0) REVERT: C 448 ASN cc_start: 0.0625 (m110) cc_final: 0.0322 (m110) REVERT: C 497 PHE cc_start: 0.4212 (OUTLIER) cc_final: 0.3033 (t80) REVERT: C 821 LEU cc_start: 0.8944 (tp) cc_final: 0.8607 (mp) REVERT: C 904 TYR cc_start: 0.8844 (m-10) cc_final: 0.8602 (m-10) REVERT: C 988 GLU cc_start: 0.8783 (tp30) cc_final: 0.8383 (tp30) REVERT: D 13 GLN cc_start: 0.8653 (pm20) cc_final: 0.8341 (pp30) REVERT: D 32 TYR cc_start: 0.8529 (m-80) cc_final: 0.8149 (m-80) REVERT: D 74 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7128 (m-40) REVERT: D 86 LEU cc_start: 0.7988 (tp) cc_final: 0.7581 (mp) REVERT: D 107 ILE cc_start: 0.7419 (mm) cc_final: 0.6960 (mm) REVERT: E 24 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8088 (ttm110) REVERT: E 78 ARG cc_start: 0.7098 (ttp80) cc_final: 0.6751 (ttp80) REVERT: H 38 ARG cc_start: 0.7988 (ptp90) cc_final: 0.7757 (ptp-110) REVERT: H 50 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7186 (mmm160) REVERT: H 54 ASP cc_start: 0.8801 (m-30) cc_final: 0.8525 (p0) REVERT: H 67 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.5682 (ptm160) REVERT: H 87 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7162 (mtt180) REVERT: H 179 PHE cc_start: 0.5042 (OUTLIER) cc_final: 0.4745 (t80) REVERT: H 207 TYR cc_start: 0.2425 (t80) cc_final: 0.1588 (m-10) REVERT: L 4 MET cc_start: 0.7055 (mmm) cc_final: 0.6680 (mmm) REVERT: L 24 ARG cc_start: 0.7990 (mpp80) cc_final: 0.7639 (mpp80) REVERT: L 88 TYR cc_start: 0.7504 (m-80) cc_final: 0.7045 (m-10) REVERT: L 139 ARG cc_start: 0.6696 (mtt-85) cc_final: 0.5852 (mmp80) REVERT: J 35 HIS cc_start: 0.8225 (m170) cc_final: 0.7876 (m170) REVERT: J 36 TRP cc_start: 0.7042 (t-100) cc_final: 0.6244 (t-100) REVERT: J 83 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6550 (mpp) REVERT: J 110 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8374 (mm-30) REVERT: J 124 VAL cc_start: 0.6432 (OUTLIER) cc_final: 0.6150 (p) REVERT: J 209 CYS cc_start: -0.2304 (OUTLIER) cc_final: -0.3263 (p) REVERT: K 4 MET cc_start: 0.7120 (mpp) cc_final: 0.6479 (mpp) REVERT: K 17 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7000 (pp20) REVERT: K 87 TYR cc_start: 0.8088 (m-80) cc_final: 0.7846 (m-80) REVERT: K 166 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5129 (ptpp) outliers start: 118 outliers final: 58 residues processed: 476 average time/residue: 0.1979 time to fit residues: 153.7874 Evaluate side-chains 434 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 358 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 179 PHE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 373 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 443 optimal weight: 30.0000 chunk 359 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088608 restraints weight = 67038.912| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.96 r_work: 0.3034 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 36773 Z= 0.232 Angle : 0.662 20.731 50183 Z= 0.322 Chirality : 0.046 0.236 5825 Planarity : 0.004 0.067 6368 Dihedral : 6.534 100.294 6293 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.45 % Allowed : 15.64 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.20 (0.13), residues: 4447 helix: 1.98 (0.20), residues: 722 sheet: 0.31 (0.14), residues: 1296 loop : -1.07 (0.12), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.022 0.002 TYR L 92 PHE 0.025 0.002 PHE L 136 TRP 0.012 0.002 TRP J 33 HIS 0.011 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00550 (36661) covalent geometry : angle 0.62386 (49895) SS BOND : bond 0.00448 ( 45) SS BOND : angle 1.91001 ( 90) hydrogen bonds : bond 0.04812 ( 1342) hydrogen bonds : angle 5.88689 ( 3684) Misc. bond : bond 0.00276 ( 1) link_BETA1-4 : bond 0.00302 ( 21) link_BETA1-4 : angle 1.67806 ( 63) link_BETA1-6 : bond 0.00092 ( 3) link_BETA1-6 : angle 1.80369 ( 9) link_NAG-ASN : bond 0.00684 ( 42) link_NAG-ASN : angle 4.04551 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 365 time to evaluate : 1.188 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: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8011 (m-30) cc_final: 0.7735 (m-30) REVERT: A 298 GLU cc_start: 0.8983 (tt0) cc_final: 0.8409 (mt-10) REVERT: A 408 ARG cc_start: 0.8824 (ppt170) cc_final: 0.8498 (ppt170) REVERT: A 420 ASP cc_start: 0.9074 (m-30) cc_final: 0.8699 (m-30) REVERT: A 423 TYR cc_start: 0.8974 (t80) cc_final: 0.8746 (t80) REVERT: A 428 ASP cc_start: 0.9187 (p0) cc_final: 0.8908 (p0) REVERT: A 465 GLU cc_start: 0.9110 (tt0) cc_final: 0.8875 (tt0) REVERT: A 571 ASP cc_start: 0.8539 (t70) cc_final: 0.8163 (t0) REVERT: A 697 MET cc_start: 0.9161 (ptm) cc_final: 0.8891 (ptm) REVERT: A 988 GLU cc_start: 0.8568 (mp0) cc_final: 0.8311 (mp0) REVERT: B 52 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 129 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7880 (mtpt) REVERT: B 170 TYR cc_start: 0.7912 (t80) cc_final: 0.7662 (t80) REVERT: B 190 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7876 (mtt90) REVERT: B 207 HIS cc_start: 0.7775 (t-170) cc_final: 0.7510 (t70) REVERT: B 239 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7308 (mm-40) REVERT: B 449 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: B 523 THR cc_start: 0.8869 (p) cc_final: 0.8462 (t) REVERT: B 529 LYS cc_start: 0.8710 (mttm) cc_final: 0.8489 (mmtp) REVERT: B 586 ASP cc_start: 0.8921 (m-30) cc_final: 0.8515 (m-30) REVERT: B 740 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8782 (ttt) REVERT: B 988 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: C 18 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.4444 (tt) REVERT: C 21 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5137 (ptt-90) REVERT: C 81 ASN cc_start: 0.8817 (p0) cc_final: 0.8392 (p0) REVERT: C 140 PHE cc_start: 0.8894 (p90) cc_final: 0.8533 (p90) REVERT: C 177 MET cc_start: -0.2364 (mmt) cc_final: -0.3936 (mpp) REVERT: C 197 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (pp) REVERT: C 202 LYS cc_start: 0.8988 (mttt) cc_final: 0.8213 (mtmm) REVERT: C 353 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7162 (p-90) REVERT: C 389 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6932 (p0) REVERT: C 497 PHE cc_start: 0.4404 (OUTLIER) cc_final: 0.3061 (t80) REVERT: D 13 GLN cc_start: 0.8694 (pm20) cc_final: 0.8329 (pp30) REVERT: D 32 TYR cc_start: 0.8655 (m-80) cc_final: 0.8258 (m-80) REVERT: D 74 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.7142 (m-40) REVERT: D 86 LEU cc_start: 0.8091 (tp) cc_final: 0.7221 (mp) REVERT: D 107 ILE cc_start: 0.7704 (mm) cc_final: 0.7315 (mm) REVERT: E 24 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8067 (ttm110) REVERT: H 38 ARG cc_start: 0.8335 (ptp90) cc_final: 0.7772 (ttm110) REVERT: H 54 ASP cc_start: 0.8862 (m-30) cc_final: 0.8533 (p0) REVERT: H 67 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.5716 (ptm160) REVERT: H 179 PHE cc_start: 0.4980 (OUTLIER) cc_final: 0.4740 (t80) REVERT: H 207 TYR cc_start: 0.2646 (t80) cc_final: 0.1707 (m-10) REVERT: L 4 MET cc_start: 0.7133 (mmm) cc_final: 0.6753 (mmm) REVERT: L 24 ARG cc_start: 0.8099 (mpp80) cc_final: 0.7724 (mpp80) REVERT: L 88 TYR cc_start: 0.7485 (m-80) cc_final: 0.7098 (m-10) REVERT: L 136 PHE cc_start: 0.8299 (p90) cc_final: 0.7561 (p90) REVERT: J 36 TRP cc_start: 0.7302 (t-100) cc_final: 0.6370 (t-100) REVERT: J 110 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8372 (mm-30) REVERT: J 124 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6231 (p) REVERT: J 208 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6481 (pt) REVERT: J 209 CYS cc_start: -0.2080 (OUTLIER) cc_final: -0.2857 (p) REVERT: K 4 MET cc_start: 0.7098 (mpp) cc_final: 0.6477 (mpp) REVERT: K 17 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6757 (pp20) REVERT: K 166 LYS cc_start: 0.5670 (OUTLIER) cc_final: 0.5005 (ptpp) outliers start: 135 outliers final: 80 residues processed: 475 average time/residue: 0.1937 time to fit residues: 150.6895 Evaluate side-chains 440 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 342 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 PHE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 38 optimal weight: 1.9990 chunk 296 optimal weight: 0.4980 chunk 231 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 429 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 188 ASN C 354 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN J 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.089433 restraints weight = 66605.170| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.18 r_work: 0.3018 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36773 Z= 0.218 Angle : 0.647 21.106 50183 Z= 0.315 Chirality : 0.046 0.240 5825 Planarity : 0.004 0.067 6368 Dihedral : 6.461 100.163 6291 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.50 % Allowed : 16.05 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.27 (0.13), residues: 4447 helix: 2.00 (0.20), residues: 714 sheet: 0.23 (0.14), residues: 1305 loop : -1.11 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 46 TYR 0.023 0.001 TYR L 137 PHE 0.020 0.002 PHE L 72 TRP 0.019 0.002 TRP A 258 HIS 0.007 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00513 (36661) covalent geometry : angle 0.61297 (49895) SS BOND : bond 0.00474 ( 45) SS BOND : angle 1.52431 ( 90) hydrogen bonds : bond 0.04622 ( 1342) hydrogen bonds : angle 5.76561 ( 3684) Misc. bond : bond 0.00293 ( 1) link_BETA1-4 : bond 0.00327 ( 21) link_BETA1-4 : angle 1.54088 ( 63) link_BETA1-6 : bond 0.00232 ( 3) link_BETA1-6 : angle 1.81769 ( 9) link_NAG-ASN : bond 0.00623 ( 42) link_NAG-ASN : angle 3.87048 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 353 time to evaluate : 1.321 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8056 (m-30) cc_final: 0.7769 (m-30) REVERT: A 408 ARG cc_start: 0.8877 (ppt170) cc_final: 0.8530 (ppt170) REVERT: A 420 ASP cc_start: 0.9092 (m-30) cc_final: 0.8678 (m-30) REVERT: A 428 ASP cc_start: 0.9217 (p0) cc_final: 0.8916 (p0) REVERT: A 571 ASP cc_start: 0.8574 (t70) cc_final: 0.8200 (t0) REVERT: A 697 MET cc_start: 0.9164 (ptm) cc_final: 0.8906 (ptm) REVERT: A 988 GLU cc_start: 0.8609 (mp0) cc_final: 0.8349 (mp0) REVERT: B 52 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 129 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7872 (mtpt) REVERT: B 190 ARG cc_start: 0.7959 (mtt90) cc_final: 0.7573 (mtt90) REVERT: B 239 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7340 (mm-40) REVERT: B 249 LEU cc_start: 0.3925 (OUTLIER) cc_final: 0.3498 (mm) REVERT: B 378 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8617 (ptmt) REVERT: B 449 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: B 523 THR cc_start: 0.8830 (p) cc_final: 0.8462 (t) REVERT: B 529 LYS cc_start: 0.8724 (mttm) cc_final: 0.8490 (mmtp) REVERT: B 564 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7426 (mm-40) REVERT: B 586 ASP cc_start: 0.8940 (m-30) cc_final: 0.8594 (m-30) REVERT: B 619 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.8898 (mp0) REVERT: B 740 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8772 (ttt) REVERT: B 988 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: C 21 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5711 (ptt180) REVERT: C 81 ASN cc_start: 0.8836 (p0) cc_final: 0.8364 (p0) REVERT: C 140 PHE cc_start: 0.8883 (p90) cc_final: 0.8354 (p90) REVERT: C 177 MET cc_start: -0.2006 (mmt) cc_final: -0.4293 (mpp) REVERT: C 197 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8606 (pp) REVERT: C 202 LYS cc_start: 0.9013 (mttt) cc_final: 0.8207 (mtmm) REVERT: C 340 GLU cc_start: 0.7957 (pp20) cc_final: 0.7554 (pt0) REVERT: C 347 PHE cc_start: 0.8081 (m-10) cc_final: 0.7311 (m-10) REVERT: C 353 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7254 (p-90) REVERT: C 408 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7760 (pmt-80) REVERT: C 497 PHE cc_start: 0.4980 (OUTLIER) cc_final: 0.3620 (t80) REVERT: D 13 GLN cc_start: 0.8676 (pm20) cc_final: 0.8328 (pp30) REVERT: D 74 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7170 (m-40) REVERT: D 107 ILE cc_start: 0.7825 (mm) cc_final: 0.7445 (mm) REVERT: D 110 GLU cc_start: 0.8661 (mp0) cc_final: 0.7838 (mp0) REVERT: E 78 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6856 (ttp80) REVERT: H 38 ARG cc_start: 0.8328 (ptp90) cc_final: 0.8125 (ptp-110) REVERT: H 54 ASP cc_start: 0.8923 (m-30) cc_final: 0.8496 (p0) REVERT: H 67 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.5608 (ptm160) REVERT: H 207 TYR cc_start: 0.2777 (t80) cc_final: 0.1875 (m-10) REVERT: H 209 CYS cc_start: 0.2926 (OUTLIER) cc_final: 0.2705 (m) REVERT: L 4 MET cc_start: 0.7037 (mmm) cc_final: 0.6767 (mmm) REVERT: L 24 ARG cc_start: 0.8108 (mpp80) cc_final: 0.7683 (mpp80) REVERT: L 88 TYR cc_start: 0.7499 (m-80) cc_final: 0.7033 (m-10) REVERT: L 136 PHE cc_start: 0.8088 (p90) cc_final: 0.7470 (p90) REVERT: L 139 ARG cc_start: 0.6472 (mpt-90) cc_final: 0.6199 (mpt-90) REVERT: J 35 HIS cc_start: 0.8429 (m170) cc_final: 0.8067 (m-70) REVERT: J 36 TRP cc_start: 0.7261 (t-100) cc_final: 0.6301 (t-100) REVERT: J 50 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6397 (ttt180) REVERT: J 110 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8064 (mp0) REVERT: J 111 TRP cc_start: 0.7491 (m100) cc_final: 0.7128 (m100) REVERT: J 124 VAL cc_start: 0.6673 (OUTLIER) cc_final: 0.6309 (p) REVERT: J 208 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6472 (pt) REVERT: J 209 CYS cc_start: -0.2109 (OUTLIER) cc_final: -0.2854 (p) REVERT: K 4 MET cc_start: 0.7132 (mpp) cc_final: 0.6471 (mpp) REVERT: K 17 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6739 (pp20) REVERT: K 166 LYS cc_start: 0.5689 (OUTLIER) cc_final: 0.5049 (ptpp) outliers start: 137 outliers final: 85 residues processed: 465 average time/residue: 0.2105 time to fit residues: 158.5153 Evaluate side-chains 444 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 339 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 209 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 318 optimal weight: 0.7980 chunk 357 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 363 optimal weight: 6.9990 chunk 346 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 207 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 409 GLN C1002 GLN D 74 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN J 184 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.155588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093074 restraints weight = 66648.557| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.18 r_work: 0.3066 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 36773 Z= 0.113 Angle : 0.601 20.798 50183 Z= 0.290 Chirality : 0.044 0.236 5825 Planarity : 0.004 0.065 6368 Dihedral : 6.018 94.819 6283 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.02 % Allowed : 16.79 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.15 (0.13), residues: 4447 helix: 2.14 (0.20), residues: 723 sheet: 0.28 (0.14), residues: 1299 loop : -1.04 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 46 TYR 0.032 0.001 TYR E 137 PHE 0.019 0.001 PHE A 140 TRP 0.015 0.001 TRP A 258 HIS 0.005 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00252 (36661) covalent geometry : angle 0.56845 (49895) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.24535 ( 90) hydrogen bonds : bond 0.03893 ( 1342) hydrogen bonds : angle 5.52347 ( 3684) Misc. bond : bond 0.00234 ( 1) link_BETA1-4 : bond 0.00393 ( 21) link_BETA1-4 : angle 1.37953 ( 63) link_BETA1-6 : bond 0.00279 ( 3) link_BETA1-6 : angle 1.77042 ( 9) link_NAG-ASN : bond 0.00553 ( 42) link_NAG-ASN : angle 3.68538 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 375 time to evaluate : 1.267 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8132 (m-30) cc_final: 0.7849 (m-30) REVERT: A 129 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7606 (mmmt) REVERT: A 298 GLU cc_start: 0.9032 (tt0) cc_final: 0.8434 (mt-10) REVERT: A 406 GLU cc_start: 0.8453 (pt0) cc_final: 0.7774 (pm20) REVERT: A 408 ARG cc_start: 0.8874 (ppt170) cc_final: 0.8550 (ppt170) REVERT: A 420 ASP cc_start: 0.9064 (m-30) cc_final: 0.8667 (m-30) REVERT: A 428 ASP cc_start: 0.9197 (p0) cc_final: 0.8941 (p0) REVERT: A 571 ASP cc_start: 0.8553 (t70) cc_final: 0.8165 (t0) REVERT: A 697 MET cc_start: 0.9159 (ptm) cc_final: 0.8905 (ptm) REVERT: A 988 GLU cc_start: 0.8657 (mp0) cc_final: 0.8384 (mp0) REVERT: B 52 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8084 (tm-30) REVERT: B 129 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7919 (mtpt) REVERT: B 190 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7667 (mtt90) REVERT: B 239 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7417 (mm-40) REVERT: B 249 LEU cc_start: 0.4020 (OUTLIER) cc_final: 0.3601 (mm) REVERT: B 378 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8588 (ptmt) REVERT: B 449 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: B 523 THR cc_start: 0.8840 (p) cc_final: 0.8468 (t) REVERT: B 586 ASP cc_start: 0.8926 (m-30) cc_final: 0.8551 (m-30) REVERT: B 740 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8740 (ttt) REVERT: B 988 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: C 21 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.4912 (ptt-90) REVERT: C 81 ASN cc_start: 0.8805 (p0) cc_final: 0.8376 (p0) REVERT: C 140 PHE cc_start: 0.8928 (p90) cc_final: 0.8495 (p90) REVERT: C 177 MET cc_start: -0.2129 (mmt) cc_final: -0.3922 (mpp) REVERT: C 197 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8569 (pp) REVERT: C 202 LYS cc_start: 0.8975 (mttt) cc_final: 0.8197 (mtmm) REVERT: C 340 GLU cc_start: 0.8023 (pp20) cc_final: 0.7622 (pt0) REVERT: C 347 PHE cc_start: 0.8079 (m-10) cc_final: 0.7386 (m-10) REVERT: C 353 TRP cc_start: 0.8253 (OUTLIER) cc_final: 0.7441 (p-90) REVERT: C 355 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.8211 (ttt90) REVERT: C 389 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6941 (p0) REVERT: C 408 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7801 (pmt-80) REVERT: C 497 PHE cc_start: 0.4365 (OUTLIER) cc_final: 0.3328 (t80) REVERT: C 508 TYR cc_start: 0.8343 (m-80) cc_final: 0.8015 (m-80) REVERT: C 821 LEU cc_start: 0.8971 (tp) cc_final: 0.8579 (mp) REVERT: C 904 TYR cc_start: 0.8871 (m-10) cc_final: 0.8606 (m-10) REVERT: C 988 GLU cc_start: 0.8793 (tp30) cc_final: 0.8346 (tp30) REVERT: D 13 GLN cc_start: 0.8698 (pm20) cc_final: 0.8356 (pp30) REVERT: D 32 TYR cc_start: 0.8645 (m-80) cc_final: 0.8165 (m-80) REVERT: D 74 ASN cc_start: 0.7280 (OUTLIER) cc_final: 0.7055 (m-40) REVERT: D 86 LEU cc_start: 0.7813 (tp) cc_final: 0.7345 (pt) REVERT: D 107 ILE cc_start: 0.7672 (mm) cc_final: 0.7298 (mm) REVERT: E 78 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6807 (ttp80) REVERT: H 50 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6835 (mmm160) REVERT: H 54 ASP cc_start: 0.8864 (m-30) cc_final: 0.8490 (p0) REVERT: H 67 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5471 (ptm160) REVERT: H 87 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6986 (mtt180) REVERT: H 98 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.7835 (ttm170) REVERT: H 179 PHE cc_start: 0.5379 (OUTLIER) cc_final: 0.5022 (t80) REVERT: H 207 TYR cc_start: 0.2787 (t80) cc_final: 0.1893 (m-10) REVERT: H 209 CYS cc_start: 0.2859 (OUTLIER) cc_final: 0.2637 (m) REVERT: L 88 TYR cc_start: 0.7550 (m-80) cc_final: 0.7066 (m-80) REVERT: L 136 PHE cc_start: 0.7905 (p90) cc_final: 0.7502 (p90) REVERT: J 35 HIS cc_start: 0.8367 (m170) cc_final: 0.7678 (m-70) REVERT: J 36 TRP cc_start: 0.7204 (OUTLIER) cc_final: 0.6244 (t-100) REVERT: J 38 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.5082 (ptm160) REVERT: J 50 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6449 (ttt180) REVERT: J 110 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8203 (mp0) REVERT: J 111 TRP cc_start: 0.7494 (m100) cc_final: 0.7070 (m100) REVERT: J 124 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6599 (p) REVERT: J 208 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6416 (pt) REVERT: J 209 CYS cc_start: -0.2162 (OUTLIER) cc_final: -0.2915 (p) REVERT: K 4 MET cc_start: 0.6952 (mpp) cc_final: 0.6261 (mpp) REVERT: K 17 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6607 (pp20) REVERT: K 166 LYS cc_start: 0.5654 (OUTLIER) cc_final: 0.4999 (ptpp) outliers start: 118 outliers final: 71 residues processed: 468 average time/residue: 0.2019 time to fit residues: 153.3955 Evaluate side-chains 442 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 346 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 PHE Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 209 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 233 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 281 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 354 optimal weight: 20.0000 chunk 414 optimal weight: 7.9990 chunk 191 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 207 HIS ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN D 74 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.155000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091567 restraints weight = 66574.020| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.93 r_work: 0.3071 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36773 Z= 0.138 Angle : 0.610 20.893 50183 Z= 0.294 Chirality : 0.045 0.237 5825 Planarity : 0.004 0.064 6368 Dihedral : 5.924 91.082 6283 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.30 % Allowed : 16.97 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.12 (0.13), residues: 4447 helix: 2.16 (0.20), residues: 723 sheet: 0.32 (0.14), residues: 1291 loop : -1.02 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 46 TYR 0.029 0.001 TYR D 112 PHE 0.023 0.001 PHE B 92 TRP 0.013 0.001 TRP A 258 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00320 (36661) covalent geometry : angle 0.57699 (49895) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.45739 ( 90) hydrogen bonds : bond 0.03959 ( 1342) hydrogen bonds : angle 5.46170 ( 3684) Misc. bond : bond 0.00239 ( 1) link_BETA1-4 : bond 0.00343 ( 21) link_BETA1-4 : angle 1.41972 ( 63) link_BETA1-6 : bond 0.00226 ( 3) link_BETA1-6 : angle 1.73116 ( 9) link_NAG-ASN : bond 0.00539 ( 42) link_NAG-ASN : angle 3.69363 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 359 time to evaluate : 1.533 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8043 (m-30) cc_final: 0.7745 (m-30) REVERT: A 129 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7639 (mmmt) REVERT: A 298 GLU cc_start: 0.9008 (tt0) cc_final: 0.8434 (mt-10) REVERT: A 408 ARG cc_start: 0.8848 (ppt170) cc_final: 0.8544 (ppt170) REVERT: A 420 ASP cc_start: 0.9041 (m-30) cc_final: 0.8657 (m-30) REVERT: A 428 ASP cc_start: 0.9178 (p0) cc_final: 0.8924 (p0) REVERT: A 571 ASP cc_start: 0.8556 (t70) cc_final: 0.8168 (t0) REVERT: A 697 MET cc_start: 0.9162 (ptm) cc_final: 0.8916 (ptm) REVERT: A 988 GLU cc_start: 0.8650 (mp0) cc_final: 0.8375 (mp0) REVERT: B 52 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 129 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7950 (mtpt) REVERT: B 135 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7105 (m-10) REVERT: B 190 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7604 (mtt90) REVERT: B 207 HIS cc_start: 0.7996 (t-90) cc_final: 0.7778 (t-90) REVERT: B 239 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7456 (mm-40) REVERT: B 249 LEU cc_start: 0.4032 (OUTLIER) cc_final: 0.3617 (mm) REVERT: B 378 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8655 (ptmm) REVERT: B 417 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8250 (ptpp) REVERT: B 449 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: B 523 THR cc_start: 0.8873 (p) cc_final: 0.8509 (t) REVERT: B 586 ASP cc_start: 0.8908 (m-30) cc_final: 0.8536 (m-30) REVERT: B 740 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8733 (ttt) REVERT: B 988 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: C 81 ASN cc_start: 0.8807 (p0) cc_final: 0.8439 (p0) REVERT: C 140 PHE cc_start: 0.8929 (p90) cc_final: 0.8550 (p90) REVERT: C 177 MET cc_start: -0.1767 (mmt) cc_final: -0.3737 (mpp) REVERT: C 197 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8525 (pp) REVERT: C 202 LYS cc_start: 0.8986 (mttt) cc_final: 0.8371 (mttp) REVERT: C 340 GLU cc_start: 0.8032 (pp20) cc_final: 0.7634 (pt0) REVERT: C 347 PHE cc_start: 0.8075 (m-10) cc_final: 0.7371 (m-10) REVERT: C 353 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7392 (p-90) REVERT: C 355 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.8151 (ttt90) REVERT: C 389 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6907 (p0) REVERT: C 408 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7809 (pmt-80) REVERT: C 497 PHE cc_start: 0.4592 (OUTLIER) cc_final: 0.3471 (t80) REVERT: C 508 TYR cc_start: 0.8282 (m-80) cc_final: 0.7998 (m-80) REVERT: C 988 GLU cc_start: 0.8771 (tp30) cc_final: 0.8343 (tp30) REVERT: D 13 GLN cc_start: 0.8700 (pm20) cc_final: 0.8349 (pp30) REVERT: D 32 TYR cc_start: 0.8653 (m-80) cc_final: 0.8168 (m-80) REVERT: D 74 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7342 (m-40) REVERT: D 86 LEU cc_start: 0.8055 (tp) cc_final: 0.7641 (pt) REVERT: D 107 ILE cc_start: 0.7700 (mm) cc_final: 0.7328 (mm) REVERT: E 78 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6814 (ttp80) REVERT: H 54 ASP cc_start: 0.8825 (m-30) cc_final: 0.8491 (p0) REVERT: H 67 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5378 (ptm160) REVERT: H 179 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.4556 (t80) REVERT: H 207 TYR cc_start: 0.2598 (t80) cc_final: 0.1767 (m-80) REVERT: L 88 TYR cc_start: 0.7500 (m-80) cc_final: 0.7069 (m-10) REVERT: L 136 PHE cc_start: 0.8122 (p90) cc_final: 0.7797 (p90) REVERT: J 35 HIS cc_start: 0.8280 (m170) cc_final: 0.7519 (m-70) REVERT: J 36 TRP cc_start: 0.7271 (t-100) cc_final: 0.6313 (t-100) REVERT: J 38 ARG cc_start: 0.5344 (OUTLIER) cc_final: 0.5023 (ptm160) REVERT: J 50 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6378 (ttt180) REVERT: J 110 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8189 (mp0) REVERT: J 124 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6538 (p) REVERT: J 208 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6302 (pt) REVERT: J 209 CYS cc_start: -0.2267 (OUTLIER) cc_final: -0.2928 (p) REVERT: K 4 MET cc_start: 0.6968 (mpp) cc_final: 0.6289 (mpp) REVERT: K 17 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6547 (pp20) REVERT: K 166 LYS cc_start: 0.5685 (OUTLIER) cc_final: 0.5000 (ptpp) outliers start: 129 outliers final: 81 residues processed: 462 average time/residue: 0.1958 time to fit residues: 148.2716 Evaluate side-chains 446 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 343 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 PHE Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 128 optimal weight: 0.0000 chunk 229 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 323 optimal weight: 0.0370 chunk 330 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 overall best weight: 0.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 239 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 957 GLN C1002 GLN D 74 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.156588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094507 restraints weight = 66908.509| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.52 r_work: 0.3041 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36773 Z= 0.105 Angle : 0.592 20.830 50183 Z= 0.286 Chirality : 0.044 0.236 5825 Planarity : 0.004 0.064 6368 Dihedral : 5.704 82.811 6283 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.02 % Allowed : 17.48 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.05 (0.13), residues: 4447 helix: 2.22 (0.20), residues: 724 sheet: 0.36 (0.14), residues: 1307 loop : -0.99 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 46 TYR 0.021 0.001 TYR L 137 PHE 0.024 0.001 PHE B 92 TRP 0.019 0.001 TRP L 145 HIS 0.009 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00231 (36661) covalent geometry : angle 0.56121 (49895) SS BOND : bond 0.00306 ( 45) SS BOND : angle 1.12974 ( 90) hydrogen bonds : bond 0.03644 ( 1342) hydrogen bonds : angle 5.34699 ( 3684) Misc. bond : bond 0.00262 ( 1) link_BETA1-4 : bond 0.00406 ( 21) link_BETA1-4 : angle 1.33044 ( 63) link_BETA1-6 : bond 0.00282 ( 3) link_BETA1-6 : angle 1.69778 ( 9) link_NAG-ASN : bond 0.00559 ( 42) link_NAG-ASN : angle 3.59653 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 366 time to evaluate : 1.298 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: symmetry clash REVERT: A 88 ASP cc_start: 0.7860 (m-30) cc_final: 0.7536 (m-30) REVERT: A 129 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7533 (mmmt) REVERT: A 298 GLU cc_start: 0.8820 (tt0) cc_final: 0.8312 (mt-10) REVERT: A 376 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 408 ARG cc_start: 0.8761 (ppt170) cc_final: 0.8459 (ppt170) REVERT: A 420 ASP cc_start: 0.8978 (m-30) cc_final: 0.8621 (m-30) REVERT: A 428 ASP cc_start: 0.9131 (p0) cc_final: 0.8885 (p0) REVERT: A 571 ASP cc_start: 0.8396 (t70) cc_final: 0.7985 (t0) REVERT: A 697 MET cc_start: 0.9056 (ptm) cc_final: 0.8787 (ptm) REVERT: A 988 GLU cc_start: 0.8468 (mp0) cc_final: 0.8172 (mp0) REVERT: B 52 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 129 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8114 (mtpt) REVERT: B 135 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7053 (m-10) REVERT: B 190 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7556 (mtt90) REVERT: B 204 TYR cc_start: 0.8605 (m-80) cc_final: 0.7896 (m-80) REVERT: B 207 HIS cc_start: 0.7789 (t-90) cc_final: 0.7532 (t-90) REVERT: B 239 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7363 (mm-40) REVERT: B 249 LEU cc_start: 0.3945 (OUTLIER) cc_final: 0.3532 (mm) REVERT: B 354 ASN cc_start: 0.8161 (t0) cc_final: 0.7836 (t0) REVERT: B 378 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8588 (ptmm) REVERT: B 417 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8242 (ptpp) REVERT: B 449 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: B 523 THR cc_start: 0.8768 (p) cc_final: 0.8434 (t) REVERT: B 586 ASP cc_start: 0.8811 (m-30) cc_final: 0.8482 (m-30) REVERT: B 619 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.8752 (mp0) REVERT: B 740 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8533 (ttt) REVERT: B 988 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: C 21 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.4880 (ptt-90) REVERT: C 52 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 81 ASN cc_start: 0.8746 (p0) cc_final: 0.8294 (p0) REVERT: C 140 PHE cc_start: 0.8916 (p90) cc_final: 0.8612 (p90) REVERT: C 177 MET cc_start: -0.1983 (mmt) cc_final: -0.3794 (mpp) REVERT: C 197 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8508 (pp) REVERT: C 202 LYS cc_start: 0.8833 (mttt) cc_final: 0.8203 (mttp) REVERT: C 340 GLU cc_start: 0.8106 (pp20) cc_final: 0.7747 (pt0) REVERT: C 347 PHE cc_start: 0.7892 (m-10) cc_final: 0.7247 (m-10) REVERT: C 353 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7009 (p-90) REVERT: C 355 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.8075 (ttt90) REVERT: C 389 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6862 (p0) REVERT: C 408 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7789 (pmt-80) REVERT: C 497 PHE cc_start: 0.3990 (OUTLIER) cc_final: 0.3007 (t80) REVERT: C 508 TYR cc_start: 0.8219 (m-80) cc_final: 0.7959 (m-80) REVERT: C 740 MET cc_start: 0.8370 (mmm) cc_final: 0.7905 (mmm) REVERT: C 904 TYR cc_start: 0.8725 (m-10) cc_final: 0.8449 (m-10) REVERT: D 13 GLN cc_start: 0.8674 (pm20) cc_final: 0.8328 (pp30) REVERT: D 32 TYR cc_start: 0.8532 (m-80) cc_final: 0.8024 (m-80) REVERT: D 74 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7573 (m110) REVERT: D 86 LEU cc_start: 0.8094 (tp) cc_final: 0.7798 (pt) REVERT: D 107 ILE cc_start: 0.7545 (mm) cc_final: 0.7168 (mm) REVERT: E 78 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6834 (ttp80) REVERT: H 50 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6663 (mmm160) REVERT: H 54 ASP cc_start: 0.8766 (m-30) cc_final: 0.8460 (p0) REVERT: H 67 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5184 (ptm160) REVERT: H 179 PHE cc_start: 0.4885 (OUTLIER) cc_final: 0.4670 (t80) REVERT: H 207 TYR cc_start: 0.2662 (t80) cc_final: 0.1746 (m-80) REVERT: L 71 ASP cc_start: 0.8812 (t0) cc_final: 0.8253 (t0) REVERT: L 88 TYR cc_start: 0.7449 (m-80) cc_final: 0.7046 (m-10) REVERT: L 136 PHE cc_start: 0.8079 (p90) cc_final: 0.7763 (p90) REVERT: J 34 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: J 35 HIS cc_start: 0.8156 (m170) cc_final: 0.7404 (m-70) REVERT: J 36 TRP cc_start: 0.7053 (t-100) cc_final: 0.6096 (t-100) REVERT: J 38 ARG cc_start: 0.5128 (OUTLIER) cc_final: 0.4852 (ptm160) REVERT: J 50 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6468 (ttt180) REVERT: J 110 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8009 (mp0) REVERT: J 124 VAL cc_start: 0.6922 (OUTLIER) cc_final: 0.6632 (p) REVERT: J 208 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6306 (pt) REVERT: J 209 CYS cc_start: -0.2256 (OUTLIER) cc_final: -0.2894 (p) REVERT: K 4 MET cc_start: 0.6826 (mpp) cc_final: 0.6180 (mpp) REVERT: K 17 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6702 (pp20) REVERT: K 166 LYS cc_start: 0.5650 (OUTLIER) cc_final: 0.4997 (ptpp) outliers start: 118 outliers final: 72 residues processed: 457 average time/residue: 0.2139 time to fit residues: 158.9443 Evaluate side-chains 447 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 348 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 179 PHE Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 207 optimal weight: 0.4980 chunk 384 optimal weight: 6.9990 chunk 181 optimal weight: 0.0770 chunk 174 optimal weight: 3.9990 chunk 339 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 357 optimal weight: 20.0000 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 957 GLN C1002 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.156044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094414 restraints weight = 66084.954| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.34 r_work: 0.3072 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36773 Z= 0.114 Angle : 0.597 20.857 50183 Z= 0.288 Chirality : 0.044 0.236 5825 Planarity : 0.004 0.064 6368 Dihedral : 5.507 76.417 6283 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 2.86 % Allowed : 17.66 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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 aren not related in a simple way. whole: -0.03 (0.13), residues: 4447 helix: 2.23 (0.20), residues: 724 sheet: 0.38 (0.14), residues: 1305 loop : -0.97 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 19 TYR 0.027 0.001 TYR D 112 PHE 0.022 0.001 PHE A 140 TRP 0.018 0.001 TRP A 258 HIS 0.009 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00258 (36661) covalent geometry : angle 0.56624 (49895) SS BOND : bond 0.00317 ( 45) SS BOND : angle 1.11400 ( 90) hydrogen bonds : bond 0.03632 ( 1342) hydrogen bonds : angle 5.29542 ( 3684) Misc. bond : bond 0.00251 ( 1) link_BETA1-4 : bond 0.00374 ( 21) link_BETA1-4 : angle 1.33322 ( 63) link_BETA1-6 : bond 0.00290 ( 3) link_BETA1-6 : angle 1.67216 ( 9) link_NAG-ASN : bond 0.00546 ( 42) link_NAG-ASN : angle 3.59565 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 360 time to evaluate : 1.212 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: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8021 (m-30) cc_final: 0.7711 (m-30) REVERT: A 129 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7584 (mmmt) REVERT: A 298 GLU cc_start: 0.9035 (tt0) cc_final: 0.8424 (mt-10) REVERT: A 376 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 408 ARG cc_start: 0.8865 (ppt170) cc_final: 0.8546 (ppt170) REVERT: A 420 ASP cc_start: 0.9059 (m-30) cc_final: 0.8677 (m-30) REVERT: A 428 ASP cc_start: 0.9217 (p0) cc_final: 0.8982 (p0) REVERT: A 571 ASP cc_start: 0.8547 (t70) cc_final: 0.8157 (t0) REVERT: A 697 MET cc_start: 0.9151 (ptm) cc_final: 0.8838 (ptm) REVERT: A 988 GLU cc_start: 0.8674 (mp0) cc_final: 0.8363 (mp0) REVERT: B 52 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 129 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8057 (mtpt) REVERT: B 135 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7227 (m-10) REVERT: B 190 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7602 (mtt90) REVERT: B 204 TYR cc_start: 0.8753 (m-80) cc_final: 0.8123 (m-80) REVERT: B 207 HIS cc_start: 0.7914 (t-90) cc_final: 0.7649 (t-90) REVERT: B 239 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7435 (mm-40) REVERT: B 249 LEU cc_start: 0.4001 (OUTLIER) cc_final: 0.3599 (mm) REVERT: B 354 ASN cc_start: 0.8284 (t0) cc_final: 0.7960 (t0) REVERT: B 417 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8230 (ptpp) REVERT: B 523 THR cc_start: 0.8762 (p) cc_final: 0.8431 (t) REVERT: B 586 ASP cc_start: 0.8887 (m-30) cc_final: 0.8574 (m-30) REVERT: B 619 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.8797 (mp0) REVERT: B 740 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8709 (ttt) REVERT: B 988 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 52 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8284 (tm-30) REVERT: C 81 ASN cc_start: 0.8787 (p0) cc_final: 0.8480 (p0) REVERT: C 140 PHE cc_start: 0.8888 (p90) cc_final: 0.8644 (p90) REVERT: C 177 MET cc_start: -0.1986 (mmt) cc_final: -0.3787 (mpp) REVERT: C 197 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8536 (pp) REVERT: C 202 LYS cc_start: 0.8983 (mttt) cc_final: 0.8372 (mttp) REVERT: C 340 GLU cc_start: 0.8124 (pp20) cc_final: 0.7777 (pt0) REVERT: C 347 PHE cc_start: 0.8024 (m-10) cc_final: 0.7496 (m-10) REVERT: C 351 TYR cc_start: 0.7882 (p90) cc_final: 0.7578 (p90) REVERT: C 353 TRP cc_start: 0.7935 (OUTLIER) cc_final: 0.7067 (p-90) REVERT: C 355 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.8146 (ttt90) REVERT: C 389 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6872 (p0) REVERT: C 408 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7831 (pmt-80) REVERT: C 409 GLN cc_start: 0.8493 (mt0) cc_final: 0.8290 (mt0) REVERT: C 497 PHE cc_start: 0.4347 (OUTLIER) cc_final: 0.3150 (t80) REVERT: C 508 TYR cc_start: 0.8340 (m-80) cc_final: 0.8086 (m-80) REVERT: C 740 MET cc_start: 0.8474 (mmm) cc_final: 0.8072 (mmm) REVERT: C 904 TYR cc_start: 0.8851 (m-10) cc_final: 0.8595 (m-10) REVERT: D 13 GLN cc_start: 0.8683 (pm20) cc_final: 0.8335 (pp30) REVERT: D 32 TYR cc_start: 0.8633 (m-80) cc_final: 0.8108 (m-80) REVERT: D 86 LEU cc_start: 0.8069 (tp) cc_final: 0.7816 (pt) REVERT: D 107 ILE cc_start: 0.7579 (mm) cc_final: 0.7214 (mm) REVERT: E 78 ARG cc_start: 0.7238 (ttp80) cc_final: 0.6848 (ttp80) REVERT: H 50 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6752 (mmm160) REVERT: H 54 ASP cc_start: 0.8849 (m-30) cc_final: 0.8553 (p0) REVERT: H 67 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.5715 (ptm160) REVERT: H 207 TYR cc_start: 0.2649 (t80) cc_final: 0.1705 (m-80) REVERT: L 4 MET cc_start: 0.6941 (tpp) cc_final: 0.6428 (tpp) REVERT: L 23 CYS cc_start: 0.6835 (t) cc_final: 0.5985 (t) REVERT: L 24 ARG cc_start: 0.7734 (mmm160) cc_final: 0.7253 (mmm160) REVERT: L 36 TRP cc_start: 0.7120 (t-100) cc_final: 0.6852 (m-90) REVERT: L 71 ASP cc_start: 0.8579 (t0) cc_final: 0.8332 (t0) REVERT: L 88 TYR cc_start: 0.7500 (m-80) cc_final: 0.7032 (m-10) REVERT: L 136 PHE cc_start: 0.8125 (p90) cc_final: 0.7792 (p90) REVERT: J 34 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8309 (mmm) REVERT: J 35 HIS cc_start: 0.8234 (m170) cc_final: 0.7473 (m-70) REVERT: J 36 TRP cc_start: 0.7146 (t-100) cc_final: 0.6176 (t-100) REVERT: J 38 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.5019 (ptm160) REVERT: J 50 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6565 (ttt180) REVERT: J 110 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8168 (mp0) REVERT: J 124 VAL cc_start: 0.6962 (OUTLIER) cc_final: 0.6669 (p) REVERT: J 208 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6359 (pt) REVERT: J 209 CYS cc_start: -0.2151 (OUTLIER) cc_final: -0.2827 (p) REVERT: K 4 MET cc_start: 0.6823 (mpp) cc_final: 0.5885 (mpp) REVERT: K 17 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: K 166 LYS cc_start: 0.5646 (OUTLIER) cc_final: 0.4985 (ptpp) outliers start: 112 outliers final: 77 residues processed: 448 average time/residue: 0.2125 time to fit residues: 155.3804 Evaluate side-chains 450 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 350 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 336 optimal weight: 20.0000 chunk 371 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 396 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 386 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 273 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 957 GLN C1002 GLN D 74 ASN D 82 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.153693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090050 restraints weight = 66373.159| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.89 r_work: 0.3048 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 36773 Z= 0.202 Angle : 0.646 21.302 50183 Z= 0.313 Chirality : 0.046 0.245 5825 Planarity : 0.004 0.071 6368 Dihedral : 5.588 78.065 6283 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 2.76 % Allowed : 17.86 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.13 (0.13), residues: 4447 helix: 2.09 (0.20), residues: 729 sheet: 0.33 (0.14), residues: 1293 loop : -1.03 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 98 TYR 0.022 0.001 TYR E 137 PHE 0.026 0.002 PHE A 92 TRP 0.015 0.002 TRP L 145 HIS 0.009 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00478 (36661) covalent geometry : angle 0.61190 (49895) SS BOND : bond 0.00447 ( 45) SS BOND : angle 1.53804 ( 90) hydrogen bonds : bond 0.04408 ( 1342) hydrogen bonds : angle 5.45830 ( 3684) Misc. bond : bond 0.00305 ( 1) link_BETA1-4 : bond 0.00295 ( 21) link_BETA1-4 : angle 1.47733 ( 63) link_BETA1-6 : bond 0.00197 ( 3) link_BETA1-6 : angle 1.71447 ( 9) link_NAG-ASN : bond 0.00624 ( 42) link_NAG-ASN : angle 3.83402 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 351 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7657 (mmmt) REVERT: A 298 GLU cc_start: 0.9023 (tt0) cc_final: 0.8458 (mt-10) REVERT: A 376 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8841 (p) REVERT: A 408 ARG cc_start: 0.8847 (ppt170) cc_final: 0.8548 (ppt170) REVERT: A 420 ASP cc_start: 0.9051 (m-30) cc_final: 0.8704 (m-30) REVERT: A 428 ASP cc_start: 0.9167 (p0) cc_final: 0.8911 (p0) REVERT: A 571 ASP cc_start: 0.8586 (t70) cc_final: 0.8188 (t0) REVERT: A 697 MET cc_start: 0.9157 (ptm) cc_final: 0.8901 (ptm) REVERT: A 988 GLU cc_start: 0.8608 (mp0) cc_final: 0.8315 (mp0) REVERT: B 52 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 129 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8126 (mtpt) REVERT: B 135 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7328 (m-10) REVERT: B 190 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7676 (mtt90) REVERT: B 207 HIS cc_start: 0.7904 (t-90) cc_final: 0.7694 (t70) REVERT: B 239 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7362 (mm-40) REVERT: B 249 LEU cc_start: 0.3969 (OUTLIER) cc_final: 0.3558 (mm) REVERT: B 378 LYS cc_start: 0.8999 (ptpp) cc_final: 0.8648 (ptmt) REVERT: B 417 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8307 (ptpp) REVERT: B 523 THR cc_start: 0.8906 (p) cc_final: 0.8580 (t) REVERT: B 586 ASP cc_start: 0.8880 (m-30) cc_final: 0.8584 (m-30) REVERT: B 619 GLU cc_start: 0.9464 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: B 740 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8729 (ttt) REVERT: B 902 MET cc_start: 0.9350 (tpt) cc_final: 0.9143 (mmt) REVERT: B 988 GLU cc_start: 0.8610 (pm20) cc_final: 0.7709 (tm-30) REVERT: C 81 ASN cc_start: 0.8802 (p0) cc_final: 0.8479 (p0) REVERT: C 140 PHE cc_start: 0.8912 (p90) cc_final: 0.8687 (p90) REVERT: C 177 MET cc_start: -0.2007 (mmt) cc_final: -0.2874 (ttt) REVERT: C 197 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8537 (pp) REVERT: C 202 LYS cc_start: 0.9019 (mttt) cc_final: 0.8381 (mttp) REVERT: C 347 PHE cc_start: 0.8180 (m-10) cc_final: 0.7370 (m-10) REVERT: C 351 TYR cc_start: 0.8015 (p90) cc_final: 0.7646 (p90) REVERT: C 353 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.7172 (p-90) REVERT: C 354 ASN cc_start: 0.7284 (m110) cc_final: 0.6988 (m110) REVERT: C 355 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.7169 (mtp-110) REVERT: C 389 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6924 (p0) REVERT: C 408 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7852 (pmt-80) REVERT: C 409 GLN cc_start: 0.8586 (mt0) cc_final: 0.8385 (mt0) REVERT: C 497 PHE cc_start: 0.4794 (OUTLIER) cc_final: 0.3704 (t80) REVERT: C 508 TYR cc_start: 0.8392 (m-80) cc_final: 0.8130 (m-80) REVERT: D 13 GLN cc_start: 0.8705 (pm20) cc_final: 0.8388 (pp30) REVERT: D 32 TYR cc_start: 0.8642 (m-80) cc_final: 0.8143 (m-80) REVERT: D 86 LEU cc_start: 0.8094 (tp) cc_final: 0.7887 (pt) REVERT: D 107 ILE cc_start: 0.7893 (mm) cc_final: 0.7536 (mm) REVERT: D 137 LEU cc_start: 0.6693 (mt) cc_final: 0.6433 (pp) REVERT: E 78 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6917 (ttp80) REVERT: L 4 MET cc_start: 0.6995 (tpp) cc_final: 0.6498 (tpp) REVERT: L 23 CYS cc_start: 0.6833 (t) cc_final: 0.6271 (t) REVERT: L 24 ARG cc_start: 0.7910 (mmm160) cc_final: 0.7427 (mmm160) REVERT: L 71 ASP cc_start: 0.8731 (t0) cc_final: 0.8390 (t0) REVERT: L 88 TYR cc_start: 0.7388 (m-80) cc_final: 0.7089 (m-10) REVERT: L 136 PHE cc_start: 0.8156 (p90) cc_final: 0.7850 (p90) REVERT: J 34 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8332 (mmm) REVERT: J 35 HIS cc_start: 0.8303 (m170) cc_final: 0.7546 (m-70) REVERT: J 36 TRP cc_start: 0.7347 (t-100) cc_final: 0.6352 (t-100) REVERT: J 38 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.5010 (ptm160) REVERT: J 50 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6367 (ttt180) REVERT: J 110 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8164 (mp0) REVERT: J 124 VAL cc_start: 0.6965 (OUTLIER) cc_final: 0.6640 (p) REVERT: J 208 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6331 (pt) REVERT: J 209 CYS cc_start: -0.2171 (OUTLIER) cc_final: -0.2838 (p) REVERT: K 4 MET cc_start: 0.6983 (mpp) cc_final: 0.6004 (mpp) REVERT: K 17 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6696 (pp20) REVERT: K 166 LYS cc_start: 0.5635 (OUTLIER) cc_final: 0.4879 (ptpp) outliers start: 108 outliers final: 74 residues processed: 437 average time/residue: 0.2185 time to fit residues: 153.4526 Evaluate side-chains 433 residues out of total 3913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 339 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 134 optimal weight: 1.9990 chunk 419 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 211 optimal weight: 30.0000 chunk 310 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 420 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 957 GLN C1002 GLN D 74 ASN D 82 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.155377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093134 restraints weight = 66516.928| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.44 r_work: 0.3021 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36773 Z= 0.125 Angle : 0.611 21.146 50183 Z= 0.295 Chirality : 0.044 0.243 5825 Planarity : 0.004 0.065 6368 Dihedral : 5.312 74.286 6281 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.53 % Allowed : 18.20 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.08 (0.13), residues: 4447 helix: 2.13 (0.20), residues: 729 sheet: 0.34 (0.14), residues: 1297 loop : -0.98 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 19 TYR 0.058 0.001 TYR E 137 PHE 0.029 0.001 PHE A 92 TRP 0.015 0.001 TRP L 145 HIS 0.008 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00285 (36661) covalent geometry : angle 0.57843 (49895) SS BOND : bond 0.00351 ( 45) SS BOND : angle 1.21792 ( 90) hydrogen bonds : bond 0.03846 ( 1342) hydrogen bonds : angle 5.33399 ( 3684) Misc. bond : bond 0.00271 ( 1) link_BETA1-4 : bond 0.00348 ( 21) link_BETA1-4 : angle 1.30997 ( 63) link_BETA1-6 : bond 0.00238 ( 3) link_BETA1-6 : angle 1.70146 ( 9) link_NAG-ASN : bond 0.00554 ( 42) link_NAG-ASN : angle 3.72015 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13688.62 seconds wall clock time: 233 minutes 14.78 seconds (13994.78 seconds total)