Starting phenix.real_space_refine on Tue Aug 26 09:26:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whu_37548/08_2025/8whu_37548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whu_37548/08_2025/8whu_37548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8whu_37548/08_2025/8whu_37548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whu_37548/08_2025/8whu_37548.map" model { file = "/net/cci-nas-00/data/ceres_data/8whu_37548/08_2025/8whu_37548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whu_37548/08_2025/8whu_37548.cif" } resolution = 3.3 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= 0.077 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 172 5.16 5 Cl 2 4.86 5 C 22674 2.51 5 N 5796 2.21 5 O 6902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 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: 35548 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8285 Classifications: {'peptide': 1059} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8285 Classifications: {'peptide': 1059} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8285 Classifications: {'peptide': 1059} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "E" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.44, per 1000 atoms: 0.18 Number of scatterers: 35548 At special positions: 0 Unit cell: (141.24, 165.85, 242.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 172 16.00 O 6902 8.00 N 5796 7.00 C 22674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 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 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 354 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 354 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 616 " " NAG B1311 " - " ASN B 234 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 354 " " NAG C1311 " - " ASN C 331 " " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 90 " " NAG D 905 " - " ASN D 322 " " NAG D 906 " - " ASN D 53 " " NAG E 903 " - " ASN E 546 " " NAG E 904 " - " ASN E 322 " " NAG E 905 " - " ASN E 53 " " NAG E 906 " - " ASN E 90 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1098 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" ND1 HIS E 378 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 374 " 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8200 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 56 sheets defined 37.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.788A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.654A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.733A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.830A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.631A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.644A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.509A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 844' Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.591A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.862A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.273A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.191A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) 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 982 removed outlier: 3.521A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.780A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.336A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1139 through 1144' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.834A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.712A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.507A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 881 removed outlier: 3.833A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.021A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.417A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.976A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.686A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.909A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.076A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.814A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 618 through 627 removed outlier: 3.781A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.638A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 868 through 885 removed outlier: 3.540A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.518A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.424A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.027A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 Processing helix chain 'C' and resid 965 through 968 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.922A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.044A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.780A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.744A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.680A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.672A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.840A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.565A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.805A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.849A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.141A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.483A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.080A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.626A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'E' and resid 20 through 52 removed outlier: 3.902A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 81 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.782A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.715A pdb=" N LYS E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.924A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.528A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.765A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 276 through 283 removed outlier: 3.902A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 283 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.926A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.274A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.593A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.070A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.165A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.521A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.838A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.594A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'E' and resid 600 through 602 No H-bonds generated for 'chain 'E' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.546A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.123A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.635A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.880A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.941A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.842A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.885A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.276A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.981A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.578A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 removed outlier: 7.292A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 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: 4.310A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.223A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.643A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 130 removed outlier: 4.809A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.134A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.134A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.198A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.545A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD5, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.591A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.899A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.585A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.589A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.149A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.073A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.571A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 397 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.356A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.907A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 551 through 555 removed outlier: 3.612A pdb=" N VAL C 551 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.421A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.579A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.255A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.641A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF6, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AF7, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.043A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.745A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AG1, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.876A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'E' and resid 347 through 352 removed outlier: 3.744A pdb=" N THR E 347 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 359 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1400 hydrogen bonds defined for protein. 3957 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: 7.57 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9648 1.33 - 1.46: 9730 1.46 - 1.59: 16796 1.59 - 1.71: 3 1.71 - 1.84: 238 Bond restraints: 36415 Sorted by residual: bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.467 0.047 5.50e-03 3.31e+04 7.29e+01 bond pdb=" CG MET D 579 " pdb=" SD MET D 579 " ideal model delta sigma weight residual 1.803 1.684 0.119 2.50e-02 1.60e+03 2.26e+01 bond pdb=" SD MET D 480 " pdb=" CE MET D 480 " ideal model delta sigma weight residual 1.791 1.678 0.113 2.50e-02 1.60e+03 2.05e+01 bond pdb=" N ILE E 468 " pdb=" CA ILE E 468 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.30e-03 1.88e+04 2.05e+01 bond pdb=" SD MET E 152 " pdb=" CE MET E 152 " ideal model delta sigma weight residual 1.791 1.689 0.102 2.50e-02 1.60e+03 1.67e+01 ... (remaining 36410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 47350 2.11 - 4.21: 1920 4.21 - 6.32: 216 6.32 - 8.42: 42 8.42 - 10.53: 8 Bond angle restraints: 49536 Sorted by residual: angle pdb=" N PRO C 579 " pdb=" CA PRO C 579 " pdb=" C PRO C 579 " ideal model delta sigma weight residual 114.92 104.39 10.53 1.19e+00 7.06e-01 7.82e+01 angle pdb=" C GLU C 340 " pdb=" N VAL C 341 " pdb=" CA VAL C 341 " ideal model delta sigma weight residual 122.66 115.69 6.97 9.70e-01 1.06e+00 5.17e+01 angle pdb=" O PRO A 792 " pdb=" C PRO A 792 " pdb=" N PRO A 793 " ideal model delta sigma weight residual 121.31 118.30 3.01 4.60e-01 4.73e+00 4.28e+01 angle pdb=" C PRO C 579 " pdb=" CA PRO C 579 " pdb=" CB PRO C 579 " ideal model delta sigma weight residual 110.00 102.75 7.25 1.12e+00 7.97e-01 4.19e+01 angle pdb=" C VAL C 395 " pdb=" N TYR C 396 " pdb=" CA TYR C 396 " ideal model delta sigma weight residual 122.93 113.77 9.16 1.45e+00 4.76e-01 3.99e+01 ... (remaining 49531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 20487 24.87 - 49.74: 1605 49.74 - 74.60: 222 74.60 - 99.47: 138 99.47 - 124.34: 74 Dihedral angle restraints: 22526 sinusoidal: 9775 harmonic: 12751 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.57 61.57 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 35.12 57.88 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 39.30 53.70 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 22523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 5601 0.179 - 0.357: 71 0.357 - 0.536: 3 0.536 - 0.714: 5 0.714 - 0.893: 4 Chirality restraints: 5684 Sorted by residual: chirality pdb=" C1 BMA R 2 " pdb=" O4 NAG R 1 " pdb=" C2 BMA R 2 " pdb=" O5 BMA R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.14e+01 chirality pdb=" C1 BMA O 2 " pdb=" O4 NAG O 1 " pdb=" C2 BMA O 2 " pdb=" O5 BMA O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.72e+01 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.99e+01 ... (remaining 5681 not shown) Planarity restraints: 6365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.219 2.00e-02 2.50e+03 1.88e-01 4.41e+02 pdb=" C7 NAG B1311 " -0.043 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.314 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.127 2.00e-02 2.50e+03 1.06e-01 1.39e+02 pdb=" C7 NAG R 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.093 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.173 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.125 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" C7 NAG M 1 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.092 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.171 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.014 2.00e-02 2.50e+03 ... (remaining 6362 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 287 2.54 - 3.13: 27773 3.13 - 3.72: 55132 3.72 - 4.31: 74467 4.31 - 4.90: 123109 Nonbonded interactions: 280768 Sorted by model distance: nonbonded pdb=" OD1 ASN B1135 " pdb=" N THR B1136 " model vdw 1.947 3.120 nonbonded pdb=" OD1 ASN B1135 " pdb=" O THR B1136 " model vdw 2.004 3.040 nonbonded pdb=" O PHE A1075 " pdb=" OG1 THR A1076 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR A 124 " pdb=" O7 NAG A1301 " model vdw 2.205 3.040 nonbonded pdb=" OE1 GLU D 227 " pdb=" OH TYR D 454 " model vdw 2.216 3.040 ... (remaining 280763 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.680 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 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 : 0.008 0.607 36535 Z= 0.425 Angle : 0.962 20.589 49839 Z= 0.566 Chirality : 0.066 0.893 5684 Planarity : 0.009 0.242 6309 Dihedral : 19.621 124.340 14191 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.02 % Favored : 92.59 % Rotamer: Outliers : 1.05 % Allowed : 19.45 % Favored : 79.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.12), residues: 4331 helix: 0.94 (0.14), residues: 1403 sheet: -1.17 (0.21), residues: 604 loop : -2.08 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.026 0.002 TYR D 521 PHE 0.066 0.002 PHE A 194 TRP 0.036 0.002 TRP C1102 HIS 0.035 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00678 (36415) covalent geometry : angle 0.90194 (49536) SS BOND : bond 0.00483 ( 45) SS BOND : angle 1.17464 ( 90) hydrogen bonds : bond 0.18672 ( 1392) hydrogen bonds : angle 7.24454 ( 3957) metal coordination : bond 0.31094 ( 4) link_BETA1-4 : bond 0.00857 ( 15) link_BETA1-4 : angle 2.34784 ( 45) link_NAG-ASN : bond 0.01092 ( 56) link_NAG-ASN : angle 5.69230 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 492 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.4080 (mm) REVERT: C 453 TYR cc_start: 0.6324 (p90) cc_final: 0.6063 (p90) REVERT: D 123 MET cc_start: -0.2288 (mpp) cc_final: -0.2585 (mpp) REVERT: E 281 LEU cc_start: -0.1380 (OUTLIER) cc_final: -0.1622 (tp) outliers start: 40 outliers final: 10 residues processed: 333 average time/residue: 0.1603 time to fit residues: 92.4264 Evaluate side-chains 264 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain E residue 281 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 432 optimal weight: 0.0870 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 50.0000 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN B 49 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 613 GLN B 901 GLN B 914 ASN B1119 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 907 ASN C1010 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.239200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.196308 restraints weight = 60169.883| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 3.29 r_work: 0.3909 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36535 Z= 0.166 Angle : 0.773 20.665 49839 Z= 0.369 Chirality : 0.050 0.528 5684 Planarity : 0.005 0.063 6309 Dihedral : 11.997 115.903 6166 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.56 % Rotamer: Outliers : 2.15 % Allowed : 18.85 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.13), residues: 4331 helix: 1.41 (0.14), residues: 1415 sheet: -0.94 (0.20), residues: 626 loop : -1.95 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.020 0.001 TYR B1067 PHE 0.032 0.002 PHE A 194 TRP 0.022 0.001 TRP A 452 HIS 0.013 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00367 (36415) covalent geometry : angle 0.69674 (49536) SS BOND : bond 0.00508 ( 45) SS BOND : angle 1.85375 ( 90) hydrogen bonds : bond 0.05776 ( 1392) hydrogen bonds : angle 5.46892 ( 3957) metal coordination : bond 0.03020 ( 4) link_BETA1-4 : bond 0.00441 ( 15) link_BETA1-4 : angle 3.65334 ( 45) link_NAG-ASN : bond 0.01039 ( 56) link_NAG-ASN : angle 5.36471 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 283 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8248 (mm110) REVERT: B 167 THR cc_start: 0.5174 (OUTLIER) cc_final: 0.4957 (m) REVERT: B 780 GLU cc_start: 0.7565 (tt0) cc_final: 0.7285 (tt0) REVERT: B 868 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8201 (tt0) REVERT: B 873 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: C 59 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7441 (t80) REVERT: C 357 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7484 (ttp80) REVERT: C 436 TRP cc_start: 0.7209 (p90) cc_final: 0.6987 (p90) REVERT: C 453 TYR cc_start: 0.7162 (p90) cc_final: 0.5916 (p90) REVERT: C 508 TYR cc_start: 0.6732 (m-80) cc_final: 0.6488 (m-80) REVERT: C 737 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7638 (p0) REVERT: C 759 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7070 (t80) outliers start: 82 outliers final: 33 residues processed: 349 average time/residue: 0.1637 time to fit residues: 100.3172 Evaluate side-chains 278 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain E residue 383 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 23 optimal weight: 0.0000 chunk 121 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 275 optimal weight: 0.0870 chunk 188 optimal weight: 0.9990 chunk 205 optimal weight: 0.0970 chunk 324 optimal weight: 8.9990 chunk 429 optimal weight: 0.8980 overall best weight: 0.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 675 GLN A1005 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 675 GLN C1010 GLN C1083 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.239993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.198138 restraints weight = 60303.271| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 3.24 r_work: 0.3931 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36535 Z= 0.123 Angle : 0.701 19.937 49839 Z= 0.329 Chirality : 0.049 0.615 5684 Planarity : 0.004 0.054 6309 Dihedral : 8.465 117.697 6152 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.62 % Allowed : 19.03 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.13), residues: 4331 helix: 1.52 (0.14), residues: 1426 sheet: -0.81 (0.21), residues: 605 loop : -1.81 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.016 0.001 TYR C1067 PHE 0.023 0.001 PHE B 592 TRP 0.061 0.001 TRP E 461 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00257 (36415) covalent geometry : angle 0.62464 (49536) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.35437 ( 90) hydrogen bonds : bond 0.04687 ( 1392) hydrogen bonds : angle 5.02759 ( 3957) metal coordination : bond 0.00301 ( 4) link_BETA1-4 : bond 0.00399 ( 15) link_BETA1-4 : angle 3.46303 ( 45) link_NAG-ASN : bond 0.00947 ( 56) link_NAG-ASN : angle 5.14264 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 268 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.4605 (m-40) cc_final: 0.4341 (m-40) REVERT: A 808 ASP cc_start: 0.7650 (t0) cc_final: 0.7394 (t0) REVERT: B 86 PHE cc_start: 0.4572 (t80) cc_final: 0.4362 (t80) REVERT: B 177 MET cc_start: 0.3131 (tmm) cc_final: 0.2787 (mtp) REVERT: B 480 CYS cc_start: 0.5600 (OUTLIER) cc_final: 0.1677 (m) REVERT: B 778 THR cc_start: 0.9036 (t) cc_final: 0.8787 (m) REVERT: B 780 GLU cc_start: 0.7489 (tt0) cc_final: 0.7113 (tt0) REVERT: B 868 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7969 (tt0) REVERT: B 873 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8333 (m-10) REVERT: C 59 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7401 (t80) REVERT: C 354 ASN cc_start: 0.6379 (t0) cc_final: 0.6165 (t0) REVERT: C 357 ARG cc_start: 0.8072 (mtp-110) cc_final: 0.7637 (ttp80) REVERT: C 387 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7379 (mt) REVERT: C 436 TRP cc_start: 0.7260 (p90) cc_final: 0.6933 (p90) REVERT: C 453 TYR cc_start: 0.7014 (p90) cc_final: 0.6041 (p90) REVERT: C 737 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7537 (p0) REVERT: C 759 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6984 (t80) REVERT: D 182 GLU cc_start: 0.3697 (OUTLIER) cc_final: 0.3404 (mp0) REVERT: D 332 MET cc_start: 0.1057 (ppp) cc_final: 0.0826 (ppp) REVERT: D 524 GLN cc_start: -0.0092 (OUTLIER) cc_final: -0.0410 (tt0) REVERT: D 610 TRP cc_start: -0.0941 (t60) cc_final: -0.1560 (t60) outliers start: 100 outliers final: 29 residues processed: 349 average time/residue: 0.1667 time to fit residues: 101.4567 Evaluate side-chains 280 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 524 GLN Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 370 optimal weight: 6.9990 chunk 122 optimal weight: 0.0670 chunk 268 optimal weight: 0.4980 chunk 163 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1088 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4901 r_free = 0.4901 target = 0.241208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.204361 restraints weight = 59224.770| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 2.87 r_work: 0.4031 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36535 Z= 0.130 Angle : 0.677 20.258 49839 Z= 0.322 Chirality : 0.048 0.603 5684 Planarity : 0.004 0.053 6309 Dihedral : 7.216 117.553 6149 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.67 % Allowed : 18.98 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.13), residues: 4331 helix: 1.56 (0.14), residues: 1442 sheet: -0.66 (0.20), residues: 626 loop : -1.81 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 115 TYR 0.016 0.001 TYR B1067 PHE 0.022 0.001 PHE B 939 TRP 0.085 0.002 TRP E 461 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00284 (36415) covalent geometry : angle 0.60391 (49536) SS BOND : bond 0.00608 ( 45) SS BOND : angle 1.21751 ( 90) hydrogen bonds : bond 0.04649 ( 1392) hydrogen bonds : angle 4.81548 ( 3957) metal coordination : bond 0.00070 ( 4) link_BETA1-4 : bond 0.00400 ( 15) link_BETA1-4 : angle 3.09077 ( 45) link_NAG-ASN : bond 0.00880 ( 56) link_NAG-ASN : angle 5.01487 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 270 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 977 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (tp) REVERT: B 177 MET cc_start: 0.3127 (tmm) cc_final: 0.2817 (mtp) REVERT: B 480 CYS cc_start: 0.5591 (OUTLIER) cc_final: 0.1682 (m) REVERT: B 778 THR cc_start: 0.9111 (t) cc_final: 0.8863 (m) REVERT: B 780 GLU cc_start: 0.7472 (tt0) cc_final: 0.7072 (tt0) REVERT: B 868 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7765 (tt0) REVERT: B 873 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8356 (m-10) REVERT: C 52 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7799 (tm-30) REVERT: C 354 ASN cc_start: 0.6392 (t0) cc_final: 0.6181 (t0) REVERT: C 357 ARG cc_start: 0.8177 (mtp-110) cc_final: 0.7737 (ttp80) REVERT: C 368 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8450 (tt) REVERT: C 377 PHE cc_start: 0.5727 (OUTLIER) cc_final: 0.4831 (t80) REVERT: C 452 TRP cc_start: 0.6725 (m100) cc_final: 0.5823 (m100) REVERT: C 591 SER cc_start: 0.6613 (m) cc_final: 0.6226 (p) REVERT: C 619 GLU cc_start: 0.7114 (tt0) cc_final: 0.6881 (tt0) REVERT: C 737 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7669 (p0) REVERT: C 759 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6816 (t80) REVERT: D 182 GLU cc_start: 0.3826 (OUTLIER) cc_final: 0.3556 (mp0) REVERT: D 323 MET cc_start: 0.2311 (tmm) cc_final: 0.1069 (tmm) REVERT: D 332 MET cc_start: 0.1288 (OUTLIER) cc_final: 0.1019 (ppp) REVERT: D 447 VAL cc_start: 0.2074 (t) cc_final: 0.1836 (t) REVERT: D 579 MET cc_start: 0.3014 (mmm) cc_final: 0.2376 (mmp) REVERT: D 610 TRP cc_start: -0.0853 (t60) cc_final: -0.1288 (t60) REVERT: E 332 MET cc_start: 0.0344 (pmm) cc_final: 0.0059 (pmm) REVERT: E 360 MET cc_start: 0.1539 (tmm) cc_final: 0.1054 (ptt) REVERT: E 557 MET cc_start: 0.0797 (OUTLIER) cc_final: 0.0373 (ppp) outliers start: 102 outliers final: 52 residues processed: 351 average time/residue: 0.1754 time to fit residues: 107.6794 Evaluate side-chains 304 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 389 optimal weight: 50.0000 chunk 125 optimal weight: 0.9980 chunk 88 optimal weight: 0.0370 chunk 271 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 340 optimal weight: 40.0000 chunk 131 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN C 755 GLN C 853 GLN C 914 ASN C 960 ASN C1010 GLN D 61 ASN D 429 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.237332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.198382 restraints weight = 58223.097| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 2.86 r_work: 0.3899 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36535 Z= 0.145 Angle : 0.678 20.176 49839 Z= 0.326 Chirality : 0.048 0.592 5684 Planarity : 0.004 0.053 6309 Dihedral : 6.919 117.482 6148 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.83 % Allowed : 19.71 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.13), residues: 4331 helix: 1.57 (0.14), residues: 1447 sheet: -0.67 (0.21), residues: 612 loop : -1.79 (0.12), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.017 0.001 TYR B 266 PHE 0.029 0.001 PHE B 541 TRP 0.021 0.001 TRP B 452 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00331 (36415) covalent geometry : angle 0.61108 (49536) SS BOND : bond 0.00367 ( 45) SS BOND : angle 1.33825 ( 90) hydrogen bonds : bond 0.04969 ( 1392) hydrogen bonds : angle 4.79888 ( 3957) metal coordination : bond 0.00041 ( 4) link_BETA1-4 : bond 0.00345 ( 15) link_BETA1-4 : angle 2.59304 ( 45) link_NAG-ASN : bond 0.00856 ( 56) link_NAG-ASN : angle 4.85970 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 261 time to evaluate : 1.286 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 480 CYS cc_start: -0.0891 (OUTLIER) cc_final: -0.2121 (t) REVERT: B 177 MET cc_start: 0.4148 (tmm) cc_final: 0.3548 (mtp) REVERT: B 323 THR cc_start: 0.7518 (p) cc_final: 0.7148 (t) REVERT: B 480 CYS cc_start: 0.5804 (OUTLIER) cc_final: 0.2150 (m) REVERT: B 780 GLU cc_start: 0.7663 (tt0) cc_final: 0.7257 (tt0) REVERT: B 868 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8136 (tt0) REVERT: B 873 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: C 52 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 327 VAL cc_start: 0.7842 (m) cc_final: 0.7617 (p) REVERT: C 354 ASN cc_start: 0.6128 (t0) cc_final: 0.5896 (t0) REVERT: C 357 ARG cc_start: 0.8100 (mtp-110) cc_final: 0.7729 (ttp80) REVERT: C 452 TRP cc_start: 0.7005 (m100) cc_final: 0.6018 (m100) REVERT: C 759 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6483 (t80) REVERT: C 934 ILE cc_start: 0.9095 (tt) cc_final: 0.8823 (tp) REVERT: D 182 GLU cc_start: 0.3808 (OUTLIER) cc_final: 0.3488 (mp0) REVERT: D 332 MET cc_start: 0.1041 (OUTLIER) cc_final: 0.0738 (ppp) REVERT: D 447 VAL cc_start: 0.2047 (t) cc_final: 0.1823 (t) REVERT: D 579 MET cc_start: 0.2758 (mmm) cc_final: 0.2205 (mmp) REVERT: D 598 GLN cc_start: -0.1753 (OUTLIER) cc_final: -0.2097 (tt0) REVERT: D 610 TRP cc_start: -0.0770 (t60) cc_final: -0.1171 (t60) REVERT: E 332 MET cc_start: 0.0169 (pmm) cc_final: -0.0057 (pmm) REVERT: E 360 MET cc_start: 0.1563 (tmm) cc_final: 0.1253 (ptt) REVERT: E 557 MET cc_start: 0.0286 (OUTLIER) cc_final: -0.0109 (ppp) outliers start: 108 outliers final: 63 residues processed: 350 average time/residue: 0.1710 time to fit residues: 105.5605 Evaluate side-chains 310 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 239 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 202 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 327 optimal weight: 20.0000 chunk 311 optimal weight: 0.8980 chunk 268 optimal weight: 0.5980 chunk 379 optimal weight: 7.9990 chunk 418 optimal weight: 0.9990 chunk 415 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 342 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 339 HIS C1010 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.236146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.196584 restraints weight = 57976.490| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 2.89 r_work: 0.3903 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36535 Z= 0.131 Angle : 0.670 20.360 49839 Z= 0.319 Chirality : 0.047 0.595 5684 Planarity : 0.004 0.054 6309 Dihedral : 6.724 117.458 6148 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.75 % Allowed : 20.31 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.13), residues: 4331 helix: 1.60 (0.14), residues: 1449 sheet: -0.57 (0.21), residues: 606 loop : -1.77 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 634 TYR 0.016 0.001 TYR B1067 PHE 0.023 0.001 PHE B 541 TRP 0.033 0.001 TRP C 633 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00292 (36415) covalent geometry : angle 0.60557 (49536) SS BOND : bond 0.00356 ( 45) SS BOND : angle 1.16541 ( 90) hydrogen bonds : bond 0.04730 ( 1392) hydrogen bonds : angle 4.68536 ( 3957) metal coordination : bond 0.00042 ( 4) link_BETA1-4 : bond 0.00332 ( 15) link_BETA1-4 : angle 2.42031 ( 45) link_NAG-ASN : bond 0.00850 ( 56) link_NAG-ASN : angle 4.75500 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 250 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7625 (t80) REVERT: A 62 VAL cc_start: 0.3587 (OUTLIER) cc_final: 0.3326 (t) REVERT: A 480 CYS cc_start: -0.0920 (OUTLIER) cc_final: -0.2187 (t) REVERT: A 1119 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6771 (p0) REVERT: B 265 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: B 323 THR cc_start: 0.7578 (p) cc_final: 0.7229 (t) REVERT: B 480 CYS cc_start: 0.5062 (OUTLIER) cc_final: 0.1513 (m) REVERT: B 778 THR cc_start: 0.9205 (t) cc_final: 0.8967 (m) REVERT: B 780 GLU cc_start: 0.7565 (tt0) cc_final: 0.7185 (tt0) REVERT: B 784 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: B 786 LYS cc_start: 0.7759 (pttm) cc_final: 0.7500 (ptpp) REVERT: B 868 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7993 (tt0) REVERT: B 873 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8405 (m-10) REVERT: C 52 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7970 (tm-30) REVERT: C 226 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6918 (tt) REVERT: C 327 VAL cc_start: 0.7897 (m) cc_final: 0.7690 (p) REVERT: C 357 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7779 (ttp80) REVERT: C 452 TRP cc_start: 0.7025 (m100) cc_final: 0.6038 (m100) REVERT: C 591 SER cc_start: 0.6997 (m) cc_final: 0.6715 (p) REVERT: C 759 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.6362 (t80) REVERT: C 867 ASP cc_start: 0.8228 (m-30) cc_final: 0.8005 (m-30) REVERT: C 1128 VAL cc_start: 0.6198 (t) cc_final: 0.5900 (t) REVERT: D 182 GLU cc_start: 0.3579 (OUTLIER) cc_final: 0.3291 (mp0) REVERT: D 323 MET cc_start: 0.2200 (tmm) cc_final: 0.1237 (tmm) REVERT: D 332 MET cc_start: 0.1051 (OUTLIER) cc_final: 0.0723 (ppp) REVERT: D 447 VAL cc_start: 0.1970 (t) cc_final: 0.1750 (t) REVERT: D 462 MET cc_start: 0.2467 (mtt) cc_final: 0.1191 (ptt) REVERT: D 579 MET cc_start: 0.2580 (mmm) cc_final: 0.2189 (mmp) REVERT: D 610 TRP cc_start: -0.0697 (t60) cc_final: -0.1060 (t60) REVERT: E 332 MET cc_start: 0.0148 (pmm) cc_final: -0.0080 (pmm) REVERT: E 360 MET cc_start: 0.1551 (tmm) cc_final: 0.1241 (ptt) REVERT: E 557 MET cc_start: 0.0359 (OUTLIER) cc_final: -0.0066 (ppp) outliers start: 105 outliers final: 69 residues processed: 337 average time/residue: 0.1566 time to fit residues: 91.5005 Evaluate side-chains 310 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 228 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 224 optimal weight: 4.9990 chunk 422 optimal weight: 7.9990 chunk 327 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 340 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 314 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 675 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN C 339 HIS C 677 GLN C1010 GLN C1083 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4820 r_free = 0.4820 target = 0.232710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.192981 restraints weight = 57171.866| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.82 r_work: 0.3805 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 36535 Z= 0.164 Angle : 0.717 19.930 49839 Z= 0.344 Chirality : 0.049 0.603 5684 Planarity : 0.005 0.054 6309 Dihedral : 6.767 117.170 6147 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.85 % Allowed : 20.34 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.13), residues: 4331 helix: 1.56 (0.14), residues: 1444 sheet: -0.58 (0.21), residues: 614 loop : -1.80 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 306 TYR 0.027 0.001 TYR A 266 PHE 0.065 0.002 PHE A 216 TRP 0.047 0.002 TRP E 271 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00380 (36415) covalent geometry : angle 0.65802 (49536) SS BOND : bond 0.00375 ( 45) SS BOND : angle 1.42816 ( 90) hydrogen bonds : bond 0.05441 ( 1392) hydrogen bonds : angle 4.75158 ( 3957) metal coordination : bond 0.00113 ( 4) link_BETA1-4 : bond 0.00326 ( 15) link_BETA1-4 : angle 2.25946 ( 45) link_NAG-ASN : bond 0.00861 ( 56) link_NAG-ASN : angle 4.73873 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 257 time to evaluate : 1.208 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 58 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8224 (t80) REVERT: A 202 LYS cc_start: 0.8093 (mttm) cc_final: 0.7851 (mppt) REVERT: A 480 CYS cc_start: -0.0973 (OUTLIER) cc_final: -0.2083 (t) REVERT: B 177 MET cc_start: 0.3008 (tmm) cc_final: 0.2378 (ptp) REVERT: B 265 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: B 437 ASN cc_start: 0.5580 (OUTLIER) cc_final: 0.4678 (p0) REVERT: B 480 CYS cc_start: 0.5292 (OUTLIER) cc_final: 0.2116 (m) REVERT: B 780 GLU cc_start: 0.8162 (tt0) cc_final: 0.7736 (tt0) REVERT: B 784 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8451 (tp40) REVERT: B 786 LYS cc_start: 0.7801 (pttm) cc_final: 0.7508 (mmtm) REVERT: B 790 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7621 (ptpp) REVERT: B 868 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8557 (tt0) REVERT: B 873 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8405 (m-10) REVERT: C 52 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8317 (tm-30) REVERT: C 264 ASP cc_start: 0.4769 (OUTLIER) cc_final: 0.4425 (p0) REVERT: C 314 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8381 (tp40) REVERT: C 327 VAL cc_start: 0.8117 (m) cc_final: 0.7897 (p) REVERT: C 357 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7932 (ttp80) REVERT: C 387 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8167 (tt) REVERT: C 452 TRP cc_start: 0.7365 (m100) cc_final: 0.6443 (m100) REVERT: C 591 SER cc_start: 0.7735 (m) cc_final: 0.7443 (p) REVERT: C 636 TYR cc_start: 0.7514 (t80) cc_final: 0.7159 (t80) REVERT: C 759 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.6991 (t80) REVERT: D 182 GLU cc_start: 0.3558 (OUTLIER) cc_final: 0.3274 (mp0) REVERT: D 323 MET cc_start: 0.2316 (tmm) cc_final: 0.1469 (tmm) REVERT: D 332 MET cc_start: 0.1088 (OUTLIER) cc_final: 0.0732 (ppp) REVERT: D 462 MET cc_start: 0.2349 (mtt) cc_final: 0.1255 (ptt) REVERT: D 579 MET cc_start: 0.2498 (mmm) cc_final: 0.1828 (mmp) REVERT: D 610 TRP cc_start: -0.0592 (t60) cc_final: -0.0942 (t60) REVERT: E 360 MET cc_start: 0.1162 (tmm) cc_final: 0.0792 (ptt) REVERT: E 474 MET cc_start: 0.0235 (tpp) cc_final: -0.0017 (tpp) outliers start: 109 outliers final: 70 residues processed: 344 average time/residue: 0.1655 time to fit residues: 99.4419 Evaluate side-chains 312 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 229 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 598 GLN Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 350 optimal weight: 50.0000 chunk 377 optimal weight: 7.9990 chunk 390 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 262 optimal weight: 0.8980 chunk 212 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 339 HIS C 762 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1083 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4781 r_free = 0.4781 target = 0.227601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4037 r_free = 0.4037 target = 0.165631 restraints weight = 56907.467| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 4.42 r_work: 0.3499 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 36535 Z= 0.152 Angle : 0.686 20.184 49839 Z= 0.331 Chirality : 0.048 0.625 5684 Planarity : 0.004 0.054 6309 Dihedral : 6.619 116.791 6147 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.96 % Allowed : 20.58 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.13), residues: 4331 helix: 1.62 (0.14), residues: 1444 sheet: -0.54 (0.21), residues: 618 loop : -1.85 (0.12), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 161 TYR 0.023 0.001 TYR A 674 PHE 0.024 0.001 PHE B 939 TRP 0.024 0.001 TRP E 271 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00353 (36415) covalent geometry : angle 0.62711 (49536) SS BOND : bond 0.00323 ( 45) SS BOND : angle 1.27368 ( 90) hydrogen bonds : bond 0.05128 ( 1392) hydrogen bonds : angle 4.64076 ( 3957) metal coordination : bond 0.00048 ( 4) link_BETA1-4 : bond 0.00377 ( 15) link_BETA1-4 : angle 2.20636 ( 45) link_NAG-ASN : bond 0.00808 ( 56) link_NAG-ASN : angle 4.65276 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 252 time to evaluate : 0.922 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 58 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8174 (t80) REVERT: A 127 PHE cc_start: 0.5976 (m-80) cc_final: 0.5480 (m-80) REVERT: A 480 CYS cc_start: -0.0687 (OUTLIER) cc_final: -0.1640 (t) REVERT: A 740 MET cc_start: 0.8596 (mmm) cc_final: 0.8386 (ttt) REVERT: B 177 MET cc_start: 0.3203 (tmm) cc_final: 0.2517 (ptp) REVERT: B 480 CYS cc_start: 0.5360 (OUTLIER) cc_final: 0.2872 (m) REVERT: B 492 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4504 (tp) REVERT: B 705 VAL cc_start: 0.7994 (p) cc_final: 0.7794 (t) REVERT: B 778 THR cc_start: 0.9381 (t) cc_final: 0.9153 (m) REVERT: B 780 GLU cc_start: 0.8114 (tt0) cc_final: 0.7617 (tt0) REVERT: B 784 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8499 (tp40) REVERT: B 786 LYS cc_start: 0.7975 (pttm) cc_final: 0.7654 (mmtm) REVERT: B 790 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7618 (ptpp) REVERT: B 868 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8647 (tt0) REVERT: B 873 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8395 (m-10) REVERT: C 33 THR cc_start: 0.8160 (p) cc_final: 0.7864 (p) REVERT: C 264 ASP cc_start: 0.4770 (OUTLIER) cc_final: 0.4319 (p0) REVERT: C 327 VAL cc_start: 0.8007 (m) cc_final: 0.7732 (p) REVERT: C 357 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7755 (ttp80) REVERT: C 452 TRP cc_start: 0.7338 (m100) cc_final: 0.6436 (m100) REVERT: C 591 SER cc_start: 0.7513 (m) cc_final: 0.7302 (p) REVERT: C 632 THR cc_start: 0.8242 (m) cc_final: 0.7969 (p) REVERT: C 636 TYR cc_start: 0.7534 (t80) cc_final: 0.7122 (t80) REVERT: C 697 MET cc_start: 0.8617 (ptm) cc_final: 0.8351 (ptp) REVERT: C 759 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.6855 (t80) REVERT: C 1039 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8806 (mtp180) REVERT: D 182 GLU cc_start: 0.3692 (OUTLIER) cc_final: 0.3412 (mp0) REVERT: D 270 MET cc_start: 0.1319 (mmp) cc_final: 0.1016 (mmp) REVERT: D 323 MET cc_start: 0.2228 (tmm) cc_final: 0.1416 (tmm) REVERT: D 332 MET cc_start: 0.1396 (OUTLIER) cc_final: 0.1078 (ppp) REVERT: D 508 ASN cc_start: 0.4533 (m110) cc_final: 0.3941 (t0) REVERT: D 579 MET cc_start: 0.2278 (mmm) cc_final: 0.1824 (mmp) REVERT: D 610 TRP cc_start: 0.0492 (t60) cc_final: 0.0165 (t60) REVERT: E 360 MET cc_start: 0.1229 (tmm) cc_final: 0.1011 (ptt) REVERT: E 474 MET cc_start: -0.0136 (tpp) cc_final: -0.0454 (mmt) outliers start: 113 outliers final: 72 residues processed: 346 average time/residue: 0.1625 time to fit residues: 97.0315 Evaluate side-chains 313 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 229 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 343 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 328 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 274 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN C 339 HIS C 755 GLN C 856 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4800 r_free = 0.4800 target = 0.233629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.191340 restraints weight = 57775.264| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.87 r_work: 0.3764 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36535 Z= 0.128 Angle : 0.665 20.200 49839 Z= 0.318 Chirality : 0.047 0.627 5684 Planarity : 0.004 0.055 6309 Dihedral : 6.412 116.207 6147 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.43 % Allowed : 21.26 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.13), residues: 4331 helix: 1.64 (0.14), residues: 1456 sheet: -0.51 (0.21), residues: 624 loop : -1.84 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.019 0.001 TYR C 365 PHE 0.024 0.001 PHE B 939 TRP 0.054 0.001 TRP D 271 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00286 (36415) covalent geometry : angle 0.60617 (49536) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.12144 ( 90) hydrogen bonds : bond 0.04772 ( 1392) hydrogen bonds : angle 4.57371 ( 3957) metal coordination : bond 0.00048 ( 4) link_BETA1-4 : bond 0.00378 ( 15) link_BETA1-4 : angle 2.18144 ( 45) link_NAG-ASN : bond 0.00809 ( 56) link_NAG-ASN : angle 4.58152 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 238 time to evaluate : 1.069 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 58 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8181 (t80) REVERT: A 127 PHE cc_start: 0.6203 (m-80) cc_final: 0.5849 (m-80) REVERT: A 480 CYS cc_start: -0.0859 (OUTLIER) cc_final: -0.2021 (t) REVERT: B 177 MET cc_start: 0.2580 (tmm) cc_final: 0.2064 (ptp) REVERT: B 437 ASN cc_start: 0.5192 (OUTLIER) cc_final: 0.4518 (p0) REVERT: B 480 CYS cc_start: 0.4215 (OUTLIER) cc_final: 0.1221 (m) REVERT: B 492 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.4324 (tp) REVERT: B 778 THR cc_start: 0.9246 (t) cc_final: 0.9018 (m) REVERT: B 780 GLU cc_start: 0.7792 (tt0) cc_final: 0.7427 (tt0) REVERT: B 784 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8336 (tp40) REVERT: B 790 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7555 (ptpp) REVERT: B 873 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: C 33 THR cc_start: 0.7991 (p) cc_final: 0.7688 (p) REVERT: C 224 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: C 327 VAL cc_start: 0.8091 (m) cc_final: 0.7871 (p) REVERT: C 357 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7695 (ttp80) REVERT: C 452 TRP cc_start: 0.7237 (m100) cc_final: 0.6457 (m100) REVERT: C 632 THR cc_start: 0.8160 (m) cc_final: 0.7933 (p) REVERT: C 636 TYR cc_start: 0.7233 (t80) cc_final: 0.6877 (t80) REVERT: C 697 MET cc_start: 0.8411 (ptm) cc_final: 0.8203 (ptp) REVERT: C 759 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6725 (t80) REVERT: C 1039 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8788 (mtp180) REVERT: D 182 GLU cc_start: 0.3626 (OUTLIER) cc_final: 0.3323 (mp0) REVERT: D 323 MET cc_start: 0.2364 (tmm) cc_final: 0.1445 (tmm) REVERT: D 332 MET cc_start: 0.1533 (OUTLIER) cc_final: 0.1253 (ppp) REVERT: D 579 MET cc_start: 0.2461 (mmm) cc_final: 0.1829 (mmp) REVERT: D 610 TRP cc_start: -0.0686 (t60) cc_final: -0.0896 (t60) REVERT: E 62 MET cc_start: -0.0907 (tpt) cc_final: -0.2462 (ttt) REVERT: E 360 MET cc_start: 0.1152 (tmm) cc_final: 0.0677 (ptt) REVERT: E 474 MET cc_start: 0.0993 (tpp) cc_final: 0.0479 (mmt) outliers start: 93 outliers final: 63 residues processed: 316 average time/residue: 0.1652 time to fit residues: 90.6107 Evaluate side-chains 297 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 19 optimal weight: 0.9980 chunk 368 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 432 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.223778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.177603 restraints weight = 57346.921| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.98 r_work: 0.3660 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36535 Z= 0.185 Angle : 0.735 19.731 49839 Z= 0.358 Chirality : 0.049 0.654 5684 Planarity : 0.005 0.056 6309 Dihedral : 6.672 116.141 6147 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.25 % Allowed : 21.57 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.13), residues: 4331 helix: 1.54 (0.14), residues: 1448 sheet: -0.45 (0.21), residues: 606 loop : -1.85 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 237 TYR 0.021 0.001 TYR B 837 PHE 0.026 0.002 PHE B 939 TRP 0.036 0.002 TRP A 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00442 (36415) covalent geometry : angle 0.67975 (49536) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.62634 ( 90) hydrogen bonds : bond 0.06020 ( 1392) hydrogen bonds : angle 4.77863 ( 3957) metal coordination : bond 0.00099 ( 4) link_BETA1-4 : bond 0.00355 ( 15) link_BETA1-4 : angle 2.17975 ( 45) link_NAG-ASN : bond 0.00797 ( 56) link_NAG-ASN : angle 4.60927 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 244 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.1000 (OUTLIER) cc_final: 0.0116 (pm20) REVERT: A 480 CYS cc_start: -0.0588 (OUTLIER) cc_final: -0.1698 (t) REVERT: B 110 LEU cc_start: 0.0530 (OUTLIER) cc_final: 0.0243 (mp) REVERT: B 177 MET cc_start: 0.2933 (tmm) cc_final: 0.2168 (ptp) REVERT: B 190 ARG cc_start: 0.6704 (mtt90) cc_final: 0.6460 (mtm-85) REVERT: B 437 ASN cc_start: 0.5226 (OUTLIER) cc_final: 0.4518 (p0) REVERT: B 480 CYS cc_start: 0.4788 (OUTLIER) cc_final: 0.1219 (m) REVERT: B 492 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.4614 (mm) REVERT: B 780 GLU cc_start: 0.8081 (tt0) cc_final: 0.7653 (tt0) REVERT: B 790 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7540 (ptpp) REVERT: C 33 THR cc_start: 0.8366 (p) cc_final: 0.7863 (p) REVERT: C 314 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8224 (tp40) REVERT: C 382 VAL cc_start: 0.8699 (t) cc_final: 0.8488 (p) REVERT: C 452 TRP cc_start: 0.7259 (m100) cc_final: 0.6453 (m100) REVERT: C 636 TYR cc_start: 0.7511 (t80) cc_final: 0.7036 (t80) REVERT: C 697 MET cc_start: 0.8541 (ptm) cc_final: 0.8288 (ptp) REVERT: C 759 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7061 (t80) REVERT: C 886 TRP cc_start: 0.8287 (p90) cc_final: 0.7885 (p90) REVERT: D 182 GLU cc_start: 0.3584 (OUTLIER) cc_final: 0.3300 (mp0) REVERT: D 323 MET cc_start: 0.2555 (tmm) cc_final: 0.1554 (tmm) REVERT: D 462 MET cc_start: 0.2486 (mtt) cc_final: 0.1364 (ptt) REVERT: D 508 ASN cc_start: 0.3230 (m110) cc_final: 0.2892 (t0) REVERT: D 579 MET cc_start: 0.2471 (mmm) cc_final: 0.1982 (mmp) REVERT: D 610 TRP cc_start: -0.0699 (t60) cc_final: -0.0912 (t60) REVERT: E 62 MET cc_start: -0.1280 (tpt) cc_final: -0.2403 (ttt) REVERT: E 152 MET cc_start: 0.0485 (tpp) cc_final: -0.0196 (tpp) REVERT: E 360 MET cc_start: 0.1102 (tmm) cc_final: 0.0635 (ptt) REVERT: E 474 MET cc_start: 0.1188 (tpp) cc_final: 0.0957 (tpp) outliers start: 86 outliers final: 63 residues processed: 315 average time/residue: 0.1580 time to fit residues: 86.5434 Evaluate side-chains 299 residues out of total 3829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 227 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 370 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 342 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 252 optimal weight: 0.0060 chunk 241 optimal weight: 0.6980 chunk 329 optimal weight: 50.0000 chunk 132 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS ** C 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4741 r_free = 0.4741 target = 0.223445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.176491 restraints weight = 56917.020| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 3.02 r_work: 0.3639 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36535 Z= 0.176 Angle : 0.714 20.287 49839 Z= 0.346 Chirality : 0.049 0.709 5684 Planarity : 0.005 0.057 6309 Dihedral : 6.612 115.701 6147 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.02 % Allowed : 21.75 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.13), residues: 4331 helix: 1.58 (0.14), residues: 1448 sheet: -0.41 (0.22), residues: 592 loop : -1.86 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 237 TYR 0.022 0.001 TYR C 421 PHE 0.045 0.002 PHE A 515 TRP 0.046 0.002 TRP A 104 HIS 0.008 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00421 (36415) covalent geometry : angle 0.65846 (49536) SS BOND : bond 0.00392 ( 45) SS BOND : angle 1.40542 ( 90) hydrogen bonds : bond 0.05466 ( 1392) hydrogen bonds : angle 4.69594 ( 3957) metal coordination : bond 0.00096 ( 4) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 2.10850 ( 45) link_NAG-ASN : bond 0.00761 ( 56) link_NAG-ASN : angle 4.59422 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7665.90 seconds wall clock time: 132 minutes 13.33 seconds (7933.33 seconds total)