Starting phenix.real_space_refine on Sat Feb 7 15:05:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4t_48905/02_2026/9n4t_48905.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4t_48905/02_2026/9n4t_48905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4t_48905/02_2026/9n4t_48905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4t_48905/02_2026/9n4t_48905.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4t_48905/02_2026/9n4t_48905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4t_48905/02_2026/9n4t_48905.cif" } resolution = 3.22 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= -0.018 sd= 1.288 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 P 18 5.49 5 S 206 5.16 5 C 21594 2.51 5 N 5388 2.21 5 O 6362 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33572 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "B" Number of atoms: 6593 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 832, 6590 Classifications: {'peptide': 832} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 798} Conformer: "B" Number of residues, atoms: 832, 6590 Classifications: {'peptide': 832} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 798} bond proxies already assigned to first conformer: 6736 Chain: "C" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "D" Number of atoms: 6593 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 832, 6590 Classifications: {'peptide': 832} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 798} Conformer: "B" Number of residues, atoms: 832, 6590 Classifications: {'peptide': 832} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 798} bond proxies already assigned to first conformer: 6736 Chain: "E" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2615 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 310} Chain breaks: 1 Chain: "F" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2615 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 310} Chain breaks: 1 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 309 Unusual residues: {'2J9': 1, 'NAG': 5, 'POV': 4} Classifications: {'peptide': 1, 'undetermined': 10} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 399 Unusual residues: {'2J9': 1, 'NAG': 4, 'POV': 6} Classifications: {'peptide': 1, 'undetermined': 11} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 205 Unusual residues: {'2J9': 1, 'NAG': 5, 'POV': 2} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 399 Unusual residues: {'2J9': 1, 'NAG': 4, 'POV': 6} Classifications: {'peptide': 1, 'undetermined': 11} Link IDs: {None: 11} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.42, per 1000 atoms: 0.43 Number of scatterers: 33572 At special positions: 0 Unit cell: (150.15, 156.75, 210.375, 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) S 206 16.00 P 18 15.00 F 4 9.00 O 6362 8.00 N 5388 7.00 C 21594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.04 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=2.02 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 72 " distance=2.04 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS F 177 " - pdb=" SG CYS F 207 " distance=2.04 Simple disulfide: pdb=" SG CYS F 234 " - pdb=" SG CYS F 256 " distance=2.02 Simple disulfide: pdb=" SG CYS F 297 " - pdb=" SG CYS F 309 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 316 " - pdb=" SG CYS F 331 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA O 3 " - " MAN O 5 " BETA1-3 " BMA K 3 " - " BMA K 4 " " BMA P 3 " - " BMA P 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A1006 " - " ASN A 67 " " NAG A1007 " - " ASN A 73 " " NAG A1008 " - " ASN A 275 " " NAG A1009 " - " ASN A 412 " " NAG A1010 " - " ASN A 751 " " NAG B1006 " - " ASN B 67 " " NAG B1007 " - " ASN B 73 " " NAG B1008 " - " ASN B 412 " " NAG B1009 " - " ASN B 751 " " NAG C1005 " - " ASN C 67 " " NAG C1006 " - " ASN C 73 " " NAG C1007 " - " ASN C 275 " " NAG C1008 " - " ASN C 412 " " NAG C1009 " - " ASN C 751 " " NAG D1009 " - " ASN D 67 " " NAG D1010 " - " ASN D 73 " " NAG D1011 " - " ASN D 412 " " NAG D1012 " - " ASN D 751 " " NAG E 601 " - " ASN E 311 " " NAG F 601 " - " ASN F 311 " " NAG G 1 " - " ASN A 378 " " NAG H 1 " - " ASN A 546 " " NAG I 1 " - " ASN B 275 " " NAG J 1 " - " ASN B 378 " " NAG K 1 " - " ASN B 546 " " NAG L 1 " - " ASN C 378 " " NAG M 1 " - " ASN C 546 " " NAG N 1 " - " ASN D 275 " " NAG O 1 " - " ASN D 378 " " NAG P 1 " - " ASN D 546 " Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 2.9 seconds 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7496 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 52 sheets defined 38.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.610A pdb=" N PHE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.847A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.627A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.692A pdb=" N LEU A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.715A pdb=" N LYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.635A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 317 through 336 removed outlier: 4.315A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.502A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 4.216A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.621A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.925A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.528A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.590A pdb=" N PHE A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 655 removed outlier: 3.991A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.501A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.668A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 716 Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.748A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 4.737A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 788 removed outlier: 3.512A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.579A pdb=" N MET A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.600A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 853 removed outlier: 3.566A pdb=" N VAL A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 removed outlier: 3.615A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.847A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.373A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.633A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.899A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.783A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.574A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.575A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.701A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.574A pdb=" N LEU B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.524A pdb=" N ARG B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.891A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 567 through 575 removed outlier: 3.540A pdb=" N LEU B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 585 Processing helix chain 'B' and resid 607 through 618 removed outlier: 3.537A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 659 removed outlier: 3.886A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 removed outlier: 3.896A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.540A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 717 removed outlier: 3.760A pdb=" N LEU B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 729 removed outlier: 3.643A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.755A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 4.037A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 822 through 849 removed outlier: 3.511A pdb=" N ALA B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 846 " --> pdb=" O PHE B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 852 No H-bonds generated for 'chain 'B' and resid 850 through 852' Processing helix chain 'B' and resid 858 through 863 Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.610A pdb=" N PHE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.847A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 removed outlier: 3.626A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.693A pdb=" N LEU C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.715A pdb=" N LYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.634A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 317 through 336 removed outlier: 4.314A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.501A pdb=" N ILE C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 472 removed outlier: 4.216A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.622A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.926A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.529A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 616 removed outlier: 3.590A pdb=" N PHE C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 615 " --> pdb=" O SER C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 655 removed outlier: 3.991A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 703 through 712 removed outlier: 3.668A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 716 Processing helix chain 'C' and resid 721 through 731 removed outlier: 3.748A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 749 removed outlier: 4.738A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 788 removed outlier: 3.512A pdb=" N GLU C 788 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 removed outlier: 3.578A pdb=" N MET C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 799 removed outlier: 3.600A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 853 removed outlier: 3.566A pdb=" N VAL C 832 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 852 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 853 " --> pdb=" O ASN C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 867 removed outlier: 3.616A pdb=" N GLU C 863 " --> pdb=" O SER C 859 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 865 " --> pdb=" O MET C 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.846A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 4.373A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.633A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.899A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.783A pdb=" N ARG D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.574A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.575A pdb=" N LEU D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.701A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.574A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.523A pdb=" N ARG D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.890A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 567 through 575 removed outlier: 3.540A pdb=" N LEU D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 585 Processing helix chain 'D' and resid 607 through 618 removed outlier: 3.536A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 659 removed outlier: 3.886A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE D 658 " --> pdb=" O ASN D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 removed outlier: 3.896A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.540A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP D 706 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 removed outlier: 3.760A pdb=" N LEU D 717 " --> pdb=" O ARG D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.644A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.755A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 789 removed outlier: 4.036A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 Processing helix chain 'D' and resid 822 through 849 removed outlier: 3.512A pdb=" N ALA D 828 " --> pdb=" O PHE D 824 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 846 " --> pdb=" O PHE D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 852 No H-bonds generated for 'chain 'D' and resid 850 through 852' Processing helix chain 'D' and resid 858 through 863 Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.850A pdb=" N LEU E 282 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 342 Processing helix chain 'E' and resid 347 through 372 removed outlier: 4.265A pdb=" N ILE E 351 " --> pdb=" O HIS E 347 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.851A pdb=" N LEU F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 342 Processing helix chain 'F' and resid 347 through 372 removed outlier: 4.266A pdb=" N ILE F 351 " --> pdb=" O HIS F 347 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 353 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.583A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.319A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.529A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 228 removed outlier: 6.456A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.597A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA7, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.407A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 446 removed outlier: 3.512A pdb=" N GLU A 460 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AB1, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.642A pdb=" N PHE A 735 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 684 through 685 removed outlier: 6.766A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 37 through 43 removed outlier: 3.711A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 131 removed outlier: 8.538A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.468A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 227 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.525A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB8, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB9, first strand: chain 'B' and resid 434 through 436 removed outlier: 5.572A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC2, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC3, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AC4, first strand: chain 'B' and resid 681 through 683 removed outlier: 6.707A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 38 through 43 removed outlier: 3.583A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.318A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU C 149 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLN C 131 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.528A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 225 through 228 removed outlier: 6.455A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.597A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AD2, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.408A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 445 through 446 removed outlier: 3.512A pdb=" N GLU C 460 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 527 through 528 Processing sheet with id=AD5, first strand: chain 'C' and resid 735 through 738 removed outlier: 3.644A pdb=" N PHE C 735 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 684 through 685 removed outlier: 6.766A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 37 through 43 removed outlier: 3.712A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 131 removed outlier: 8.538A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.469A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 227 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.524A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 392 through 395 Processing sheet with id=AE3, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AE4, first strand: chain 'D' and resid 434 through 436 removed outlier: 5.571A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE6, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE7, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AE8, first strand: chain 'D' and resid 681 through 683 removed outlier: 6.707A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.605A pdb=" N THR E 87 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 155 " --> pdb=" O THR E 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'E' and resid 207 through 212 removed outlier: 4.088A pdb=" N CYS E 207 " --> pdb=" O MET E 274 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 272 " --> pdb=" O TRP E 209 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 273 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 240 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA E 253 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 223 through 227 Processing sheet with id=AF3, first strand: chain 'E' and resid 301 through 304 removed outlier: 3.831A pdb=" N PHE E 302 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE E 310 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 304 " --> pdb=" O MET E 308 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET E 308 " --> pdb=" O CYS E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 87 through 88 removed outlier: 3.604A pdb=" N THR F 87 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS F 155 " --> pdb=" O THR F 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 207 through 212 removed outlier: 4.088A pdb=" N CYS F 207 " --> pdb=" O MET F 274 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 272 " --> pdb=" O TRP F 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG F 273 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 240 " --> pdb=" O ARG F 273 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA F 253 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 223 through 227 Processing sheet with id=AF7, first strand: chain 'F' and resid 301 through 304 removed outlier: 3.830A pdb=" N PHE F 302 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 310 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS F 304 " --> pdb=" O MET F 308 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET F 308 " --> pdb=" O CYS F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 961 hydrogen bonds defined for protein. 2735 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: 7.34 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5312 1.31 - 1.44: 9238 1.44 - 1.57: 19361 1.57 - 1.70: 49 1.70 - 1.83: 332 Bond restraints: 34292 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.541 -0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.540 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C ASN C 557 " pdb=" N PRO C 558 " ideal model delta sigma weight residual 1.336 1.405 -0.070 1.08e-02 8.57e+03 4.15e+01 bond pdb=" C ASN A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.336 1.405 -0.069 1.08e-02 8.57e+03 4.05e+01 bond pdb=" C ASN D 557 " pdb=" N PRO D 558 " ideal model delta sigma weight residual 1.336 1.399 -0.064 1.08e-02 8.57e+03 3.48e+01 ... (remaining 34287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 44702 3.28 - 6.56: 1234 6.56 - 9.83: 231 9.83 - 13.11: 73 13.11 - 16.39: 12 Bond angle restraints: 46252 Sorted by residual: angle pdb=" N GLY F 46 " pdb=" CA GLY F 46 " pdb=" C GLY F 46 " ideal model delta sigma weight residual 110.21 117.51 -7.30 9.10e-01 1.21e+00 6.44e+01 angle pdb=" N GLY E 46 " pdb=" CA GLY E 46 " pdb=" C GLY E 46 " ideal model delta sigma weight residual 110.21 117.47 -7.26 9.10e-01 1.21e+00 6.36e+01 angle pdb=" C GLN A 872 " pdb=" N ARG A 873 " pdb=" CA ARG A 873 " ideal model delta sigma weight residual 121.54 135.12 -13.58 1.91e+00 2.74e-01 5.06e+01 angle pdb=" C GLN C 872 " pdb=" N ARG C 873 " pdb=" CA ARG C 873 " ideal model delta sigma weight residual 121.54 135.12 -13.58 1.91e+00 2.74e-01 5.05e+01 angle pdb=" C ASP D 598 " pdb=" N SER D 599 " pdb=" CA SER D 599 " ideal model delta sigma weight residual 121.54 133.99 -12.45 1.91e+00 2.74e-01 4.25e+01 ... (remaining 46247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 20706 35.42 - 70.85: 645 70.85 - 106.27: 189 106.27 - 141.70: 41 141.70 - 177.12: 3 Dihedral angle restraints: 21584 sinusoidal: 9940 harmonic: 11644 Sorted by residual: dihedral pdb=" CA LYS C 870 " pdb=" C LYS C 870 " pdb=" N CYS C 871 " pdb=" CA CYS C 871 " ideal model delta harmonic sigma weight residual -180.00 -132.86 -47.14 0 5.00e+00 4.00e-02 8.89e+01 dihedral pdb=" CA LYS A 870 " pdb=" C LYS A 870 " pdb=" N CYS A 871 " pdb=" CA CYS A 871 " ideal model delta harmonic sigma weight residual -180.00 -132.86 -47.14 0 5.00e+00 4.00e-02 8.89e+01 dihedral pdb=" CA PRO E 68 " pdb=" C PRO E 68 " pdb=" N ASN E 69 " pdb=" CA ASN E 69 " ideal model delta harmonic sigma weight residual -180.00 -134.31 -45.69 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 21581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 4961 0.129 - 0.258: 180 0.258 - 0.387: 29 0.387 - 0.516: 6 0.516 - 0.645: 6 Chirality restraints: 5182 Sorted by residual: chirality pdb=" C1 NAG C1005 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG C1005 " pdb=" O5 NAG C1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 378 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.11e+00 ... (remaining 5179 not shown) Planarity restraints: 5748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 295 " 0.065 5.00e-02 4.00e+02 9.86e-02 1.55e+01 pdb=" N PRO F 296 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO F 296 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 296 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 295 " -0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO E 296 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO E 296 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 296 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 35 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C VAL B 35 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL B 35 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 36 " 0.022 2.00e-02 2.50e+03 ... (remaining 5745 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7811 2.79 - 3.31: 29042 3.31 - 3.84: 53221 3.84 - 4.37: 64805 4.37 - 4.90: 108896 Nonbonded interactions: 263775 Sorted by model distance: nonbonded pdb=" NZ LYS A 531 " pdb=" O SER D 530 " model vdw 2.257 3.120 nonbonded pdb=" OG SER D 393 " pdb=" O7 NAG N 1 " model vdw 2.257 3.040 nonbonded pdb=" O VAL C 716 " pdb=" OH TYR C 733 " model vdw 2.258 3.040 nonbonded pdb=" O VAL A 716 " pdb=" OH TYR A 733 " model vdw 2.258 3.040 nonbonded pdb=" OG SER B 393 " pdb=" O7 NAG I 1 " model vdw 2.260 3.040 ... (remaining 263770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 470 or resid 472 through 864 or resid 1004 or r \ esid 1008)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 864 or resid 1005 or r \ esid 1009)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 864 or resid 1004 or r \ esid 1008)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 864 or resid 1005 or r \ esid 1009)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 6.410 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: 0.060 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 42.800 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.009 0.135 34370 Z= 0.426 Angle : 1.447 21.518 46464 Z= 0.754 Chirality : 0.066 0.645 5182 Planarity : 0.007 0.099 5718 Dihedral : 18.652 177.125 14022 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.63 % Favored : 88.50 % Rotamer: Outliers : 0.57 % Allowed : 4.92 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 2.41 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.82 (0.10), residues: 3994 helix: -4.60 (0.05), residues: 1482 sheet: -3.30 (0.20), residues: 488 loop : -3.40 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 280 TYR 0.032 0.003 TYR D 702 PHE 0.047 0.003 PHE B 735 TRP 0.035 0.004 TRP B 134 HIS 0.017 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00863 (34292) covalent geometry : angle 1.41576 (46252) SS BOND : bond 0.00457 ( 22) SS BOND : angle 1.43169 ( 44) hydrogen bonds : bond 0.30542 ( 961) hydrogen bonds : angle 10.56431 ( 2735) link_ALPHA1-3 : bond 0.01610 ( 4) link_ALPHA1-3 : angle 3.28408 ( 12) link_ALPHA1-6 : bond 0.00379 ( 4) link_ALPHA1-6 : angle 1.61573 ( 12) link_BETA1-3 : bond 0.01164 ( 2) link_BETA1-3 : angle 5.71017 ( 6) link_BETA1-4 : bond 0.01254 ( 16) link_BETA1-4 : angle 4.17862 ( 48) link_NAG-ASN : bond 0.01461 ( 30) link_NAG-ASN : angle 6.06328 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 780 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8822 (t80) cc_final: 0.8559 (t80) REVERT: A 86 TYR cc_start: 0.8225 (m-80) cc_final: 0.7648 (m-80) REVERT: A 113 SER cc_start: 0.8893 (m) cc_final: 0.8564 (p) REVERT: A 247 MET cc_start: 0.8349 (mmm) cc_final: 0.8118 (mmm) REVERT: A 434 ILE cc_start: 0.7638 (mm) cc_final: 0.7087 (mp) REVERT: A 467 LEU cc_start: 0.8218 (tp) cc_final: 0.7976 (tp) REVERT: A 485 ASP cc_start: 0.7422 (m-30) cc_final: 0.7174 (t70) REVERT: A 487 LYS cc_start: 0.8241 (tttt) cc_final: 0.7782 (tttm) REVERT: A 542 TYR cc_start: 0.6309 (t80) cc_final: 0.6085 (t80) REVERT: A 566 TYR cc_start: 0.7807 (m-80) cc_final: 0.7518 (m-80) REVERT: A 776 ASP cc_start: 0.7181 (m-30) cc_final: 0.6469 (m-30) REVERT: A 780 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7100 (mp) REVERT: A 861 MET cc_start: 0.7087 (mmp) cc_final: 0.6789 (mtt) REVERT: A 867 MET cc_start: 0.7343 (mpt) cc_final: 0.6647 (ppp) REVERT: B 53 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7404 (mp0) REVERT: B 112 SER cc_start: 0.9029 (m) cc_final: 0.8738 (p) REVERT: B 152 ASP cc_start: 0.7657 (t70) cc_final: 0.7444 (t70) REVERT: B 267 GLU cc_start: 0.8091 (tp30) cc_final: 0.7821 (tp30) REVERT: B 287 THR cc_start: 0.8663 (m) cc_final: 0.8244 (t) REVERT: B 337 PHE cc_start: 0.8736 (t80) cc_final: 0.8526 (t80) REVERT: B 457 ASP cc_start: 0.8150 (t70) cc_final: 0.7945 (t70) REVERT: B 499 ASN cc_start: 0.7649 (m110) cc_final: 0.7403 (m-40) REVERT: B 727 ARG cc_start: 0.7233 (ttm-80) cc_final: 0.6922 (ttt-90) REVERT: B 792 HIS cc_start: 0.8301 (t70) cc_final: 0.8092 (t-90) REVERT: B 818 GLN cc_start: 0.8366 (pt0) cc_final: 0.8075 (pm20) REVERT: B 841 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7264 (mt-10) REVERT: C 247 MET cc_start: 0.8330 (mmm) cc_final: 0.8024 (mmm) REVERT: C 270 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7169 (ttp-110) REVERT: C 337 PHE cc_start: 0.8500 (t80) cc_final: 0.8233 (t80) REVERT: C 485 ASP cc_start: 0.7503 (m-30) cc_final: 0.7272 (t70) REVERT: C 487 LYS cc_start: 0.8227 (tttt) cc_final: 0.7829 (tttm) REVERT: C 542 TYR cc_start: 0.6424 (t80) cc_final: 0.6130 (t80) REVERT: C 565 MET cc_start: 0.7154 (mmt) cc_final: 0.6954 (mmt) REVERT: C 780 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7084 (mp) REVERT: C 867 MET cc_start: 0.7098 (mpt) cc_final: 0.6403 (ptm) REVERT: D 53 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7418 (mp0) REVERT: D 112 SER cc_start: 0.9003 (m) cc_final: 0.8669 (t) REVERT: D 170 LYS cc_start: 0.8259 (mmtm) cc_final: 0.8009 (mmtm) REVERT: D 267 GLU cc_start: 0.8008 (tp30) cc_final: 0.7655 (tp30) REVERT: D 319 ASP cc_start: 0.7725 (m-30) cc_final: 0.7446 (m-30) REVERT: D 360 MET cc_start: 0.8227 (tpt) cc_final: 0.8006 (tpt) REVERT: D 499 ASN cc_start: 0.7576 (m110) cc_final: 0.7280 (m-40) REVERT: D 566 TYR cc_start: 0.7884 (m-80) cc_final: 0.7585 (m-80) REVERT: D 629 LYS cc_start: 0.7188 (mttp) cc_final: 0.6932 (mptt) REVERT: D 727 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.7056 (ttt-90) REVERT: D 792 HIS cc_start: 0.8029 (t70) cc_final: 0.7593 (t-170) REVERT: D 818 GLN cc_start: 0.8093 (pt0) cc_final: 0.7883 (pm20) REVERT: F 73 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7603 (pt) REVERT: F 359 LEU cc_start: 0.6968 (tm) cc_final: 0.5925 (tp) outliers start: 18 outliers final: 2 residues processed: 793 average time/residue: 0.2440 time to fit residues: 304.9798 Evaluate side-chains 435 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 430 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 495 ASN A 499 ASN A 591 ASN A 596 ASN A 604 ASN A 610 ASN A 622 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN B 593 HIS B 596 ASN B 621 GLN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 495 ASN C 499 ASN C 549 ASN C 596 ASN C 604 ASN C 610 ASN C 621 GLN C 622 GLN C 749 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN D 593 HIS D 596 ASN D 604 ASN ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 69 ASN E 227 GLN E 317 ASN F 69 ASN F 227 GLN F 307 ASN F 317 ASN F 329 ASN F 330 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.192113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145694 restraints weight = 60604.287| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.23 r_work: 0.3396 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34370 Z= 0.156 Angle : 0.870 17.372 46464 Z= 0.418 Chirality : 0.052 0.531 5182 Planarity : 0.006 0.094 5718 Dihedral : 20.138 176.082 6386 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.33 % Favored : 89.42 % Rotamer: Outliers : 1.40 % Allowed : 10.81 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.11), residues: 3994 helix: -2.76 (0.10), residues: 1472 sheet: -2.89 (0.21), residues: 476 loop : -2.99 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 349 TYR 0.029 0.002 TYR B 566 PHE 0.032 0.002 PHE B 735 TRP 0.022 0.002 TRP B 498 HIS 0.010 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00341 (34292) covalent geometry : angle 0.83251 (46252) SS BOND : bond 0.00573 ( 22) SS BOND : angle 2.51940 ( 44) hydrogen bonds : bond 0.04666 ( 961) hydrogen bonds : angle 5.35461 ( 2735) link_ALPHA1-3 : bond 0.02213 ( 4) link_ALPHA1-3 : angle 2.51890 ( 12) link_ALPHA1-6 : bond 0.00699 ( 4) link_ALPHA1-6 : angle 3.06099 ( 12) link_BETA1-3 : bond 0.00695 ( 2) link_BETA1-3 : angle 7.65235 ( 6) link_BETA1-4 : bond 0.00738 ( 16) link_BETA1-4 : angle 3.18897 ( 48) link_NAG-ASN : bond 0.01126 ( 30) link_NAG-ASN : angle 4.43488 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 515 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 TYR cc_start: 0.6882 (t80) cc_final: 0.6612 (t80) REVERT: A 780 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7110 (mp) REVERT: A 867 MET cc_start: 0.7642 (mpt) cc_final: 0.6810 (ppp) REVERT: C 542 TYR cc_start: 0.6949 (t80) cc_final: 0.6675 (t80) REVERT: C 780 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7154 (mp) REVERT: C 867 MET cc_start: 0.7070 (mpt) cc_final: 0.6428 (ppp) REVERT: D 198 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7669 (ttt90) REVERT: D 360 MET cc_start: 0.8307 (tpt) cc_final: 0.7803 (tpp) REVERT: D 792 HIS cc_start: 0.8417 (t70) cc_final: 0.8149 (t-170) REVERT: D 861 MET cc_start: 0.4856 (ptt) cc_final: 0.4366 (mtm) REVERT: E 71 GLU cc_start: 0.7068 (tp30) cc_final: 0.6867 (tp30) REVERT: E 101 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7479 (mtm110) REVERT: F 194 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6240 (mm-30) outliers start: 47 outliers final: 23 residues processed: 544 average time/residue: 0.2179 time to fit residues: 192.6639 Evaluate side-chains 430 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 405 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 42 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 292 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 591 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 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 = 0.4204 r_free = 0.4204 target = 0.188734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143207 restraints weight = 63775.948| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.08 r_work: 0.3320 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34370 Z= 0.174 Angle : 0.837 17.811 46464 Z= 0.396 Chirality : 0.052 0.519 5182 Planarity : 0.005 0.091 5718 Dihedral : 17.692 170.782 6384 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.03 % Favored : 88.72 % Rotamer: Outliers : 2.09 % Allowed : 11.75 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.12), residues: 3994 helix: -1.47 (0.12), residues: 1486 sheet: -2.70 (0.22), residues: 492 loop : -2.78 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 300 TYR 0.027 0.002 TYR C 521 PHE 0.033 0.002 PHE D 584 TRP 0.021 0.002 TRP B 706 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00407 (34292) covalent geometry : angle 0.80065 (46252) SS BOND : bond 0.00304 ( 22) SS BOND : angle 2.22033 ( 44) hydrogen bonds : bond 0.03915 ( 961) hydrogen bonds : angle 4.74906 ( 2735) link_ALPHA1-3 : bond 0.02299 ( 4) link_ALPHA1-3 : angle 2.61051 ( 12) link_ALPHA1-6 : bond 0.01376 ( 4) link_ALPHA1-6 : angle 2.70857 ( 12) link_BETA1-3 : bond 0.00593 ( 2) link_BETA1-3 : angle 7.42129 ( 6) link_BETA1-4 : bond 0.00771 ( 16) link_BETA1-4 : angle 2.90340 ( 48) link_NAG-ASN : bond 0.01017 ( 30) link_NAG-ASN : angle 4.46909 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 425 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 TYR cc_start: 0.7029 (t80) cc_final: 0.6709 (t80) REVERT: A 861 MET cc_start: 0.6916 (tmm) cc_final: 0.6659 (mmp) REVERT: A 867 MET cc_start: 0.7620 (mpt) cc_final: 0.6811 (ppp) REVERT: B 53 GLU cc_start: 0.8215 (mt-10) cc_final: 0.8001 (mp0) REVERT: B 531 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8185 (tttp) REVERT: B 572 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8861 (mm) REVERT: B 603 GLU cc_start: 0.8174 (pp20) cc_final: 0.7746 (pp20) REVERT: C 542 TYR cc_start: 0.7031 (t80) cc_final: 0.6672 (t80) REVERT: C 797 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8150 (ttpt) REVERT: C 867 MET cc_start: 0.6968 (mpt) cc_final: 0.6420 (ppp) REVERT: D 531 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8384 (mmtp) REVERT: D 861 MET cc_start: 0.4751 (ptt) cc_final: 0.4460 (mtm) REVERT: E 101 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7482 (mtm110) REVERT: E 378 MET cc_start: 0.5889 (mmm) cc_final: 0.5645 (mmp) REVERT: F 90 GLU cc_start: 0.7446 (pp20) cc_final: 0.7203 (pp20) REVERT: F 194 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6291 (mm-30) REVERT: F 242 TYR cc_start: 0.7101 (m-80) cc_final: 0.6869 (m-10) REVERT: F 274 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6393 (ttp) outliers start: 71 outliers final: 37 residues processed: 479 average time/residue: 0.2135 time to fit residues: 169.4965 Evaluate side-chains 426 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 385 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 195 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 243 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 363 optimal weight: 0.0980 chunk 367 optimal weight: 7.9990 chunk 285 optimal weight: 0.9980 chunk 327 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 381 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS B 367 HIS ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.188150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150426 restraints weight = 52292.811| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 4.17 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34370 Z= 0.169 Angle : 0.799 18.345 46464 Z= 0.377 Chirality : 0.050 0.505 5182 Planarity : 0.005 0.087 5718 Dihedral : 16.085 163.750 6380 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.30 % Rotamer: Outliers : 1.97 % Allowed : 12.44 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.13), residues: 3994 helix: -0.83 (0.13), residues: 1488 sheet: -2.34 (0.24), residues: 442 loop : -2.67 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 300 TYR 0.031 0.002 TYR E 62 PHE 0.029 0.002 PHE A 842 TRP 0.018 0.002 TRP C 353 HIS 0.007 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00396 (34292) covalent geometry : angle 0.75923 (46252) SS BOND : bond 0.00331 ( 22) SS BOND : angle 1.89237 ( 44) hydrogen bonds : bond 0.03378 ( 961) hydrogen bonds : angle 4.51541 ( 2735) link_ALPHA1-3 : bond 0.02327 ( 4) link_ALPHA1-3 : angle 2.57049 ( 12) link_ALPHA1-6 : bond 0.01665 ( 4) link_ALPHA1-6 : angle 2.26315 ( 12) link_BETA1-3 : bond 0.00354 ( 2) link_BETA1-3 : angle 7.45306 ( 6) link_BETA1-4 : bond 0.00702 ( 16) link_BETA1-4 : angle 2.75911 ( 48) link_NAG-ASN : bond 0.00909 ( 30) link_NAG-ASN : angle 4.75424 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 426 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 867 MET cc_start: 0.7707 (mpt) cc_final: 0.7087 (ppp) REVERT: B 603 GLU cc_start: 0.8094 (pp20) cc_final: 0.7823 (pp20) REVERT: C 867 MET cc_start: 0.7133 (mpt) cc_final: 0.6806 (ppp) REVERT: D 141 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8420 (t0) REVERT: E 93 TYR cc_start: 0.6156 (t80) cc_final: 0.5657 (t80) REVERT: F 66 TYR cc_start: 0.7089 (p90) cc_final: 0.6811 (p90) outliers start: 67 outliers final: 43 residues processed: 477 average time/residue: 0.2078 time to fit residues: 163.9329 Evaluate side-chains 427 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 383 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 329 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 276 optimal weight: 0.4980 chunk 229 optimal weight: 0.0770 chunk 222 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 322 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 137 GLN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN F 321 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.189970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149959 restraints weight = 66993.994| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.95 r_work: 0.3331 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34370 Z= 0.129 Angle : 0.753 18.600 46464 Z= 0.356 Chirality : 0.048 0.491 5182 Planarity : 0.005 0.085 5718 Dihedral : 15.200 156.357 6380 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.43 % Favored : 89.40 % Rotamer: Outliers : 1.72 % Allowed : 13.15 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.13), residues: 3994 helix: -0.35 (0.13), residues: 1492 sheet: -2.15 (0.24), residues: 440 loop : -2.56 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 503 TYR 0.026 0.002 TYR D 566 PHE 0.030 0.001 PHE A 842 TRP 0.017 0.001 TRP A 613 HIS 0.006 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00283 (34292) covalent geometry : angle 0.71340 (46252) SS BOND : bond 0.00266 ( 22) SS BOND : angle 1.76810 ( 44) hydrogen bonds : bond 0.03058 ( 961) hydrogen bonds : angle 4.36149 ( 2735) link_ALPHA1-3 : bond 0.02410 ( 4) link_ALPHA1-3 : angle 2.60401 ( 12) link_ALPHA1-6 : bond 0.01251 ( 4) link_ALPHA1-6 : angle 1.59512 ( 12) link_BETA1-3 : bond 0.00506 ( 2) link_BETA1-3 : angle 7.49125 ( 6) link_BETA1-4 : bond 0.00656 ( 16) link_BETA1-4 : angle 2.72825 ( 48) link_NAG-ASN : bond 0.00842 ( 30) link_NAG-ASN : angle 4.51277 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 394 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 867 MET cc_start: 0.7612 (mpt) cc_final: 0.6677 (ppp) REVERT: B 55 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 603 GLU cc_start: 0.8289 (pp20) cc_final: 0.7870 (pp20) REVERT: C 247 MET cc_start: 0.8425 (mmm) cc_final: 0.8146 (mmm) REVERT: C 867 MET cc_start: 0.6918 (mpt) cc_final: 0.6355 (ppp) REVERT: D 198 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7440 (ttt90) REVERT: D 603 GLU cc_start: 0.7884 (pp20) cc_final: 0.7166 (pp20) REVERT: E 378 MET cc_start: 0.5753 (mmm) cc_final: 0.5505 (mmp) REVERT: F 66 TYR cc_start: 0.7867 (p90) cc_final: 0.6951 (p90) REVERT: F 137 MET cc_start: 0.4992 (tpp) cc_final: 0.4418 (tpp) outliers start: 58 outliers final: 41 residues processed: 435 average time/residue: 0.2040 time to fit residues: 149.4260 Evaluate side-chains 417 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 375 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 285 optimal weight: 4.9990 chunk 326 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 277 optimal weight: 0.7980 chunk 178 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 GLN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.190418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149580 restraints weight = 69705.674| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.01 r_work: 0.3324 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34370 Z= 0.129 Angle : 0.733 18.820 46464 Z= 0.348 Chirality : 0.048 0.486 5182 Planarity : 0.005 0.083 5718 Dihedral : 14.391 145.216 6380 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.28 % Favored : 89.60 % Rotamer: Outliers : 2.03 % Allowed : 13.21 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.13), residues: 3994 helix: 0.00 (0.14), residues: 1484 sheet: -2.00 (0.25), residues: 436 loop : -2.49 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 194 TYR 0.019 0.002 TYR C 844 PHE 0.031 0.001 PHE A 842 TRP 0.017 0.001 TRP A 613 HIS 0.008 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00289 (34292) covalent geometry : angle 0.69760 (46252) SS BOND : bond 0.00390 ( 22) SS BOND : angle 1.64576 ( 44) hydrogen bonds : bond 0.02953 ( 961) hydrogen bonds : angle 4.24012 ( 2735) link_ALPHA1-3 : bond 0.02349 ( 4) link_ALPHA1-3 : angle 2.70269 ( 12) link_ALPHA1-6 : bond 0.00760 ( 4) link_ALPHA1-6 : angle 1.44934 ( 12) link_BETA1-3 : bond 0.00531 ( 2) link_BETA1-3 : angle 7.47914 ( 6) link_BETA1-4 : bond 0.00675 ( 16) link_BETA1-4 : angle 2.74234 ( 48) link_NAG-ASN : bond 0.00802 ( 30) link_NAG-ASN : angle 4.15799 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 393 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 861 MET cc_start: 0.6493 (tmm) cc_final: 0.6204 (mmt) REVERT: A 867 MET cc_start: 0.7779 (mpt) cc_final: 0.6815 (ppp) REVERT: B 603 GLU cc_start: 0.8335 (pp20) cc_final: 0.7917 (pp20) REVERT: C 247 MET cc_start: 0.8399 (mmm) cc_final: 0.8117 (mmm) REVERT: C 709 MET cc_start: 0.7648 (mtp) cc_final: 0.7387 (mtt) REVERT: C 867 MET cc_start: 0.7094 (mpt) cc_final: 0.6525 (ppp) REVERT: D 198 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7502 (ttt90) REVERT: D 399 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8307 (mt) REVERT: D 603 GLU cc_start: 0.7991 (pp20) cc_final: 0.7306 (pp20) REVERT: E 228 MET cc_start: 0.5902 (mmt) cc_final: 0.5534 (mmt) REVERT: E 378 MET cc_start: 0.6017 (mmm) cc_final: 0.5810 (mmp) REVERT: F 93 TYR cc_start: 0.6738 (t80) cc_final: 0.6495 (t80) REVERT: F 124 MET cc_start: 0.7572 (mmm) cc_final: 0.7074 (mmt) REVERT: F 137 MET cc_start: 0.4951 (tpp) cc_final: 0.4560 (tpp) outliers start: 69 outliers final: 50 residues processed: 437 average time/residue: 0.2036 time to fit residues: 149.6587 Evaluate side-chains 418 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 263 optimal weight: 0.9990 chunk 364 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.189190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148194 restraints weight = 66353.930| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.98 r_work: 0.3309 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34370 Z= 0.142 Angle : 0.733 19.854 46464 Z= 0.347 Chirality : 0.048 0.476 5182 Planarity : 0.005 0.082 5718 Dihedral : 13.998 140.491 6380 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.45 % Favored : 89.42 % Rotamer: Outliers : 1.83 % Allowed : 13.58 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 3994 helix: 0.13 (0.14), residues: 1486 sheet: -1.97 (0.25), residues: 438 loop : -2.44 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 748 TYR 0.025 0.002 TYR B 566 PHE 0.030 0.001 PHE A 842 TRP 0.015 0.001 TRP A 613 HIS 0.011 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00329 (34292) covalent geometry : angle 0.69798 (46252) SS BOND : bond 0.00283 ( 22) SS BOND : angle 1.73368 ( 44) hydrogen bonds : bond 0.02935 ( 961) hydrogen bonds : angle 4.18917 ( 2735) link_ALPHA1-3 : bond 0.02469 ( 4) link_ALPHA1-3 : angle 2.86728 ( 12) link_ALPHA1-6 : bond 0.00815 ( 4) link_ALPHA1-6 : angle 1.49307 ( 12) link_BETA1-3 : bond 0.00606 ( 2) link_BETA1-3 : angle 7.36763 ( 6) link_BETA1-4 : bond 0.00637 ( 16) link_BETA1-4 : angle 2.79251 ( 48) link_NAG-ASN : bond 0.00807 ( 30) link_NAG-ASN : angle 4.01493 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 380 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 861 MET cc_start: 0.6501 (tmm) cc_final: 0.6211 (mmt) REVERT: A 867 MET cc_start: 0.7720 (mpt) cc_final: 0.6752 (ptm) REVERT: B 603 GLU cc_start: 0.8393 (pp20) cc_final: 0.8019 (pp20) REVERT: C 247 MET cc_start: 0.8462 (mmm) cc_final: 0.8163 (mmm) REVERT: C 867 MET cc_start: 0.7007 (mpt) cc_final: 0.6395 (ppp) REVERT: D 198 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7510 (ttt90) REVERT: D 603 GLU cc_start: 0.8022 (pp20) cc_final: 0.7289 (pp20) REVERT: D 780 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8073 (mt) REVERT: E 378 MET cc_start: 0.6096 (mmm) cc_final: 0.5765 (mmp) REVERT: F 66 TYR cc_start: 0.7721 (p90) cc_final: 0.7031 (p90) REVERT: F 93 TYR cc_start: 0.6783 (t80) cc_final: 0.6392 (t80) REVERT: F 124 MET cc_start: 0.7731 (mmm) cc_final: 0.7199 (mmt) REVERT: F 272 ILE cc_start: 0.6792 (mt) cc_final: 0.6566 (mt) outliers start: 62 outliers final: 48 residues processed: 424 average time/residue: 0.2131 time to fit residues: 154.0778 Evaluate side-chains 416 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 367 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 256 CYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 159 optimal weight: 2.9990 chunk 365 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 122 optimal weight: 0.0170 chunk 292 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 328 optimal weight: 0.0050 overall best weight: 1.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 GLN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.187619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145676 restraints weight = 67882.623| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.01 r_work: 0.3285 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34370 Z= 0.168 Angle : 0.747 20.461 46464 Z= 0.354 Chirality : 0.049 0.467 5182 Planarity : 0.005 0.080 5718 Dihedral : 13.662 140.212 6380 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.88 % Favored : 89.02 % Rotamer: Outliers : 1.80 % Allowed : 13.72 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.13), residues: 3994 helix: 0.18 (0.14), residues: 1484 sheet: -2.02 (0.25), residues: 458 loop : -2.39 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 300 TYR 0.019 0.002 TYR C 702 PHE 0.031 0.002 PHE B 337 TRP 0.017 0.001 TRP D 798 HIS 0.010 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00402 (34292) covalent geometry : angle 0.71470 (46252) SS BOND : bond 0.00258 ( 22) SS BOND : angle 1.38041 ( 44) hydrogen bonds : bond 0.03065 ( 961) hydrogen bonds : angle 4.19932 ( 2735) link_ALPHA1-3 : bond 0.02612 ( 4) link_ALPHA1-3 : angle 2.88490 ( 12) link_ALPHA1-6 : bond 0.00724 ( 4) link_ALPHA1-6 : angle 1.49613 ( 12) link_BETA1-3 : bond 0.00618 ( 2) link_BETA1-3 : angle 7.12291 ( 6) link_BETA1-4 : bond 0.00568 ( 16) link_BETA1-4 : angle 2.89651 ( 48) link_NAG-ASN : bond 0.00780 ( 30) link_NAG-ASN : angle 3.88350 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 373 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 861 MET cc_start: 0.6495 (tmm) cc_final: 0.6149 (mmt) REVERT: A 867 MET cc_start: 0.7563 (mpt) cc_final: 0.6667 (ppp) REVERT: B 337 PHE cc_start: 0.8708 (t80) cc_final: 0.8505 (t80) REVERT: B 603 GLU cc_start: 0.8468 (pp20) cc_final: 0.7986 (pp20) REVERT: C 867 MET cc_start: 0.6908 (mpt) cc_final: 0.6376 (ppp) REVERT: D 55 LEU cc_start: 0.8862 (mm) cc_final: 0.8580 (mp) REVERT: D 587 TYR cc_start: 0.8349 (m-80) cc_final: 0.8078 (m-80) REVERT: D 603 GLU cc_start: 0.8107 (pp20) cc_final: 0.7328 (pp20) REVERT: D 669 ASP cc_start: 0.7952 (t0) cc_final: 0.7572 (t0) REVERT: D 780 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7998 (mt) REVERT: E 209 TRP cc_start: 0.8060 (m-90) cc_final: 0.7631 (m-90) REVERT: E 378 MET cc_start: 0.6122 (mmm) cc_final: 0.5838 (mmp) REVERT: F 66 TYR cc_start: 0.7846 (p90) cc_final: 0.7023 (p90) REVERT: F 93 TYR cc_start: 0.6766 (t80) cc_final: 0.6359 (t80) REVERT: F 124 MET cc_start: 0.7916 (mmm) cc_final: 0.7400 (mmt) REVERT: F 137 MET cc_start: 0.5015 (tpp) cc_final: 0.4755 (tpp) REVERT: F 272 ILE cc_start: 0.6501 (mt) cc_final: 0.6108 (mm) outliers start: 61 outliers final: 50 residues processed: 416 average time/residue: 0.2100 time to fit residues: 146.7308 Evaluate side-chains 416 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 256 CYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 549 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 GLN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.187669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148097 restraints weight = 69115.429| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.88 r_work: 0.3280 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34370 Z= 0.161 Angle : 0.740 20.323 46464 Z= 0.350 Chirality : 0.048 0.460 5182 Planarity : 0.005 0.080 5718 Dihedral : 13.430 140.282 6380 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.50 % Favored : 89.40 % Rotamer: Outliers : 1.92 % Allowed : 13.75 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 3994 helix: 0.19 (0.14), residues: 1496 sheet: -1.93 (0.25), residues: 438 loop : -2.38 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 748 TYR 0.032 0.002 TYR B 566 PHE 0.031 0.001 PHE A 842 TRP 0.015 0.001 TRP C 353 HIS 0.010 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00383 (34292) covalent geometry : angle 0.70931 (46252) SS BOND : bond 0.00271 ( 22) SS BOND : angle 1.35862 ( 44) hydrogen bonds : bond 0.03023 ( 961) hydrogen bonds : angle 4.19077 ( 2735) link_ALPHA1-3 : bond 0.02601 ( 4) link_ALPHA1-3 : angle 2.87400 ( 12) link_ALPHA1-6 : bond 0.00720 ( 4) link_ALPHA1-6 : angle 1.44401 ( 12) link_BETA1-3 : bond 0.00610 ( 2) link_BETA1-3 : angle 6.89387 ( 6) link_BETA1-4 : bond 0.00594 ( 16) link_BETA1-4 : angle 2.80658 ( 48) link_NAG-ASN : bond 0.00788 ( 30) link_NAG-ASN : angle 3.79981 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 375 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 861 MET cc_start: 0.6574 (tmm) cc_final: 0.6165 (mmt) REVERT: A 867 MET cc_start: 0.7610 (mpt) cc_final: 0.6704 (ppp) REVERT: B 337 PHE cc_start: 0.8402 (t80) cc_final: 0.8105 (t80) REVERT: B 603 GLU cc_start: 0.8477 (pp20) cc_final: 0.7983 (pp20) REVERT: C 55 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8632 (mt) REVERT: C 867 MET cc_start: 0.6984 (mpt) cc_final: 0.6477 (ppp) REVERT: D 55 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8471 (mt) REVERT: D 587 TYR cc_start: 0.8349 (m-80) cc_final: 0.8076 (m-80) REVERT: D 603 GLU cc_start: 0.8128 (pp20) cc_final: 0.7375 (pp20) REVERT: D 669 ASP cc_start: 0.8040 (t0) cc_final: 0.7600 (t0) REVERT: D 780 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7987 (mt) REVERT: E 209 TRP cc_start: 0.8025 (m-90) cc_final: 0.7603 (m-90) REVERT: E 378 MET cc_start: 0.6119 (mmm) cc_final: 0.5830 (mmp) REVERT: F 66 TYR cc_start: 0.7838 (p90) cc_final: 0.7026 (p90) REVERT: F 93 TYR cc_start: 0.6753 (t80) cc_final: 0.6390 (t80) REVERT: F 137 MET cc_start: 0.4894 (tpp) cc_final: 0.4666 (tpp) REVERT: F 272 ILE cc_start: 0.6581 (mt) cc_final: 0.6206 (mm) outliers start: 65 outliers final: 52 residues processed: 421 average time/residue: 0.2035 time to fit residues: 144.1956 Evaluate side-chains 419 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 364 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 256 CYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 45 CYS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 234 CYS Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 247 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 276 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 23 optimal weight: 0.0060 chunk 142 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 279 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 549 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.190111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150625 restraints weight = 65705.446| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.80 r_work: 0.3350 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34370 Z= 0.124 Angle : 0.713 19.885 46464 Z= 0.337 Chirality : 0.047 0.445 5182 Planarity : 0.005 0.079 5718 Dihedral : 13.031 140.773 6380 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.10 % Favored : 89.80 % Rotamer: Outliers : 1.52 % Allowed : 14.29 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 3994 helix: 0.36 (0.14), residues: 1502 sheet: -1.81 (0.26), residues: 438 loop : -2.35 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 198 TYR 0.021 0.001 TYR C 844 PHE 0.031 0.001 PHE A 842 TRP 0.018 0.001 TRP A 613 HIS 0.011 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00280 (34292) covalent geometry : angle 0.68311 (46252) SS BOND : bond 0.00324 ( 22) SS BOND : angle 1.22336 ( 44) hydrogen bonds : bond 0.02805 ( 961) hydrogen bonds : angle 4.13337 ( 2735) link_ALPHA1-3 : bond 0.02620 ( 4) link_ALPHA1-3 : angle 2.83452 ( 12) link_ALPHA1-6 : bond 0.00756 ( 4) link_ALPHA1-6 : angle 1.38091 ( 12) link_BETA1-3 : bond 0.00642 ( 2) link_BETA1-3 : angle 6.57652 ( 6) link_BETA1-4 : bond 0.00601 ( 16) link_BETA1-4 : angle 2.69120 ( 48) link_NAG-ASN : bond 0.00795 ( 30) link_NAG-ASN : angle 3.69711 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7988 Ramachandran restraints generated. 3994 Oldfield, 0 Emsley, 3994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 391 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 861 MET cc_start: 0.6557 (tmm) cc_final: 0.6144 (mmt) REVERT: A 867 MET cc_start: 0.7693 (mpt) cc_final: 0.6727 (ppp) REVERT: B 603 GLU cc_start: 0.8390 (pp20) cc_final: 0.7989 (pp20) REVERT: B 861 MET cc_start: 0.3307 (mpp) cc_final: 0.2979 (mtm) REVERT: C 247 MET cc_start: 0.8446 (mmm) cc_final: 0.8195 (mmm) REVERT: C 867 MET cc_start: 0.7132 (mpt) cc_final: 0.6584 (ppp) REVERT: D 198 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7282 (ttt90) REVERT: D 399 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8370 (mt) REVERT: D 587 TYR cc_start: 0.8317 (m-80) cc_final: 0.8053 (m-80) REVERT: D 603 GLU cc_start: 0.8083 (pp20) cc_final: 0.7393 (pp20) REVERT: D 669 ASP cc_start: 0.7841 (t0) cc_final: 0.7423 (t0) REVERT: D 780 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8116 (mt) REVERT: D 796 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8019 (mp0) REVERT: E 209 TRP cc_start: 0.7856 (m-90) cc_final: 0.7471 (m-90) REVERT: E 378 MET cc_start: 0.6207 (mmm) cc_final: 0.5934 (mmp) REVERT: F 66 TYR cc_start: 0.7757 (p90) cc_final: 0.7098 (p90) REVERT: F 93 TYR cc_start: 0.6787 (t80) cc_final: 0.6247 (t80) REVERT: F 137 MET cc_start: 0.4593 (tpp) cc_final: 0.4362 (tpp) REVERT: F 272 ILE cc_start: 0.6774 (mt) cc_final: 0.6441 (mm) outliers start: 51 outliers final: 40 residues processed: 423 average time/residue: 0.2097 time to fit residues: 148.7298 Evaluate side-chains 412 residues out of total 3490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 370 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 234 CYS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain F residue 45 CYS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 364 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 386 optimal weight: 5.9990 chunk 214 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 67 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 549 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 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 = 0.4216 r_free = 0.4216 target = 0.190004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147685 restraints weight = 63226.766| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.91 r_work: 0.3341 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34370 Z= 0.128 Angle : 0.707 19.880 46464 Z= 0.334 Chirality : 0.047 0.447 5182 Planarity : 0.005 0.079 5718 Dihedral : 12.795 140.565 6380 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.05 % Favored : 89.85 % Rotamer: Outliers : 1.49 % Allowed : 14.44 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3994 helix: 0.46 (0.14), residues: 1508 sheet: -1.87 (0.25), residues: 452 loop : -2.31 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 300 TYR 0.029 0.001 TYR A 702 PHE 0.032 0.001 PHE A 842 TRP 0.027 0.001 TRP D 798 HIS 0.011 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00293 (34292) covalent geometry : angle 0.67752 (46252) SS BOND : bond 0.00347 ( 22) SS BOND : angle 1.46352 ( 44) hydrogen bonds : bond 0.02798 ( 961) hydrogen bonds : angle 4.11376 ( 2735) link_ALPHA1-3 : bond 0.02646 ( 4) link_ALPHA1-3 : angle 2.90441 ( 12) link_ALPHA1-6 : bond 0.00755 ( 4) link_ALPHA1-6 : angle 1.39357 ( 12) link_BETA1-3 : bond 0.00652 ( 2) link_BETA1-3 : angle 6.30619 ( 6) link_BETA1-4 : bond 0.00588 ( 16) link_BETA1-4 : angle 2.68045 ( 48) link_NAG-ASN : bond 0.00768 ( 30) link_NAG-ASN : angle 3.62248 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9345.34 seconds wall clock time: 160 minutes 49.96 seconds (9649.96 seconds total)