Starting phenix.real_space_refine on Sat Feb 7 08:12:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4s_48904/02_2026/9n4s_48904.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4s_48904/02_2026/9n4s_48904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4s_48904/02_2026/9n4s_48904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4s_48904/02_2026/9n4s_48904.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4s_48904/02_2026/9n4s_48904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4s_48904/02_2026/9n4s_48904.cif" } resolution = 3.34 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= -0.014 sd= 1.262 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 17 5.49 5 S 185 5.16 5 C 19945 2.51 5 N 4961 2.21 5 O 5888 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31000 Number of models: 1 Model: "" Number of chains: 20 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: 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: "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: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" 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: "K" 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: "L" 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: "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: 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: "O" 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: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 361 Unusual residues: {'2J9': 1, 'NAG': 5, 'POV': 5} Classifications: {'peptide': 1, 'undetermined': 11} Link IDs: {None: 11} 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: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 311 Unusual residues: {'2J9': 2, 'NAG': 4, 'POV': 4} Classifications: {'peptide': 1, 'undetermined': 10} Link IDs: {None: 10} 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: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'NAG': 5, 'POV': 2} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} 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 Time building chain proxies: 12.22, per 1000 atoms: 0.39 Number of scatterers: 31000 At special positions: 0 Unit cell: (131.175, 159.225, 218.625, 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 185 16.00 P 17 15.00 F 4 9.00 O 5888 8.00 N 4961 7.00 C 19945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 122 " distance=2.02 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=2.03 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.04 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.04 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " BMA N 3 " - " MAN N 5 " BETA1-3 " BMA J 3 " - " BMA J 4 " " BMA L 3 " - " BMA L 4 " " BMA O 3 " - " BMA O 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 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 C1004 " - " ASN C 67 " " NAG C1005 " - " ASN C 73 " " NAG C1006 " - " ASN C 275 " " NAG C1007 " - " ASN C 412 " " NAG C1008 " - " 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 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 546 " " NAG H 1 " - " ASN B 275 " " NAG I 1 " - " ASN B 378 " " NAG J 1 " - " ASN B 546 " " NAG K 1 " - " ASN C 378 " " NAG L 1 " - " ASN C 546 " " NAG M 1 " - " ASN D 275 " " NAG N 1 " - " ASN D 378 " " NAG O 1 " - " ASN D 546 " Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 2.1 seconds 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6900 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 49 sheets defined 40.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.555A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.691A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.221A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.968A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 removed outlier: 4.372A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.348A pdb=" N GLY A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.504A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.529A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.726A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.754A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.548A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.736A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.508A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.845A pdb=" N GLY A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 652 removed outlier: 3.740A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.510A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.914A pdb=" N TRP A 706 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.537A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.741A pdb=" N GLU A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 788 removed outlier: 4.228A pdb=" N ILE A 780 " --> pdb=" O ASP A 776 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.741A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 850 Processing helix chain 'A' and resid 855 through 868 removed outlier: 3.597A pdb=" N ALA A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 868 " --> pdb=" O GLU A 864 " (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 114 through 126 removed outlier: 3.555A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.690A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 167 " --> pdb=" O LEU B 163 " (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 190 through 195 removed outlier: 4.221A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.968A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 4.372A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 4.348A pdb=" N GLY B 273 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 300 removed outlier: 3.504A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.529A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.727A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.755A pdb=" N LEU B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.548A pdb=" N ARG B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.737A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 585 removed outlier: 3.508A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.844A pdb=" N GLY B 617 " --> pdb=" O TRP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 652 removed outlier: 3.741A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.511A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.914A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.538A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.741A pdb=" N GLU B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 788 removed outlier: 4.228A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.741A pdb=" N LYS B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 853 removed outlier: 4.108A pdb=" N GLN B 851 " --> pdb=" O LYS B 847 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B 852 " --> pdb=" O LYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 864 removed outlier: 4.072A pdb=" N GLU B 863 " --> pdb=" O SER B 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.556A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 removed outlier: 3.691A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.221A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.968A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 4.373A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 4.349A pdb=" N GLY C 273 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 removed outlier: 3.504A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.528A pdb=" N LEU C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.726A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 474 removed outlier: 3.755A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.547A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.737A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.508A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.845A pdb=" N GLY C 617 " --> pdb=" O TRP C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 652 removed outlier: 3.741A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 removed outlier: 3.510A pdb=" N LEU C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 696 Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.914A pdb=" N TRP C 706 " --> pdb=" O TYR C 702 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.538A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.740A pdb=" N GLU C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 748 " --> pdb=" O PHE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 788 removed outlier: 4.228A pdb=" N ILE C 780 " --> pdb=" O ASP C 776 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.741A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 850 Processing helix chain 'C' and resid 858 through 868 removed outlier: 3.894A pdb=" N SER C 868 " --> pdb=" O GLU C 864 " (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 114 through 126 removed outlier: 3.555A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.690A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 167 " --> pdb=" O LEU D 163 " (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 190 through 195 removed outlier: 4.221A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.968A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 4.371A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 4.348A pdb=" N GLY D 273 " --> pdb=" O ARG D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 300 removed outlier: 3.503A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.529A pdb=" N LEU D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.727A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.755A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.548A pdb=" N ARG D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.736A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 585 removed outlier: 3.508A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.845A pdb=" N GLY D 617 " --> pdb=" O TRP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 652 removed outlier: 3.741A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.509A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.914A pdb=" N TRP D 706 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.538A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.741A pdb=" N GLU D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 788 removed outlier: 4.228A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 785 " --> pdb=" O ALA D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.741A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 853 removed outlier: 4.081A pdb=" N GLN D 851 " --> pdb=" O LYS D 847 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D 852 " --> pdb=" O LYS D 848 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 853 " --> pdb=" O ASN D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 868 removed outlier: 3.817A pdb=" N SER D 859 " --> pdb=" O ARG D 855 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 860 " --> pdb=" O SER D 856 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG D 866 " --> pdb=" O VAL D 862 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET D 867 " --> pdb=" O GLU D 863 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 868 " --> pdb=" O GLU D 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.703A pdb=" N CYS E 100 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.855A pdb=" N ARG E 281 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU E 282 " --> pdb=" O GLY E 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 282' Processing helix chain 'E' and resid 347 through 371 removed outlier: 4.120A pdb=" N GLY E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 43 removed outlier: 7.770A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.506A 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: 6.068A 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: 3.506A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 395 Processing sheet with id=AA7, first strand: chain 'A' and resid 434 through 436 removed outlier: 5.892A 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 Processing sheet with id=AA9, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AB1, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.662A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 38 through 43 removed outlier: 7.769A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.505A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 225 through 228 removed outlier: 6.070A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.505A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB9, first strand: chain 'B' and resid 434 through 436 removed outlier: 5.891A 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 736 through 738 removed outlier: 3.662A 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: 7.769A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC7, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.506A 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: 6.069A 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: 3.506A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AD2, first strand: chain 'C' and resid 434 through 436 removed outlier: 5.891A 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 Processing sheet with id=AD4, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD5, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AD6, first strand: chain 'C' and resid 736 through 738 removed outlier: 3.662A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 38 through 43 removed outlier: 7.770A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AD9, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.506A pdb=" N TYR D 176 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 225 through 228 removed outlier: 6.069A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.506A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 392 through 395 Processing sheet with id=AE4, first strand: chain 'D' and resid 434 through 436 removed outlier: 5.892A 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 736 through 738 removed outlier: 3.662A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 72 through 74 Processing sheet with id=AF1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF2, first strand: chain 'E' and resid 186 through 189 removed outlier: 3.751A pdb=" N GLY E 186 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE E 289 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 188 " --> pdb=" O MET E 287 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 288 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE E 223 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR E 290 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU E 221 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE E 292 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE E 219 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 205 through 210 removed outlier: 3.500A pdb=" N CYS E 207 " --> pdb=" O MET E 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET E 274 " --> pdb=" O CYS E 207 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 272 " --> pdb=" O TRP E 209 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR E 242 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 240 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA E 253 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP E 243 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU E 251 " --> pdb=" O ASP E 243 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 301 through 302 949 hydrogen bonds defined for protein. 2762 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: 5.85 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4887 1.30 - 1.43: 8398 1.43 - 1.56: 17990 1.56 - 1.69: 79 1.69 - 1.82: 304 Bond restraints: 31658 Sorted by residual: bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C3 BMA O 3 " pdb=" O3 BMA O 3 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.514 -0.108 2.00e-02 2.50e+03 2.92e+01 ... (remaining 31653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 40780 2.99 - 5.99: 1537 5.99 - 8.98: 271 8.98 - 11.98: 87 11.98 - 14.97: 26 Bond angle restraints: 42701 Sorted by residual: angle pdb=" C VAL A 661 " pdb=" N GLU A 662 " pdb=" CA GLU A 662 " ideal model delta sigma weight residual 121.40 132.88 -11.48 1.52e+00 4.33e-01 5.70e+01 angle pdb=" CA LYS C 420 " pdb=" CB LYS C 420 " pdb=" CG LYS C 420 " ideal model delta sigma weight residual 114.10 126.95 -12.85 2.00e+00 2.50e-01 4.13e+01 angle pdb=" C GLY C 803 " pdb=" N CYS C 804 " pdb=" CA CYS C 804 " ideal model delta sigma weight residual 120.83 128.85 -8.02 1.43e+00 4.89e-01 3.14e+01 angle pdb=" C GLY A 803 " pdb=" N CYS A 804 " pdb=" CA CYS A 804 " ideal model delta sigma weight residual 120.83 128.82 -7.99 1.43e+00 4.89e-01 3.12e+01 angle pdb=" C SER D 416 " pdb=" N GLN D 417 " pdb=" CA GLN D 417 " ideal model delta sigma weight residual 121.54 132.14 -10.60 1.91e+00 2.74e-01 3.08e+01 ... (remaining 42696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 19085 34.32 - 68.63: 647 68.63 - 102.95: 181 102.95 - 137.27: 62 137.27 - 171.58: 8 Dihedral angle restraints: 19983 sinusoidal: 9263 harmonic: 10720 Sorted by residual: dihedral pdb=" CA GLU A 415 " pdb=" C GLU A 415 " pdb=" N SER A 416 " pdb=" CA SER A 416 " ideal model delta harmonic sigma weight residual -180.00 -116.55 -63.45 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA THR A 660 " pdb=" C THR A 660 " pdb=" N VAL A 661 " pdb=" CA VAL A 661 " ideal model delta harmonic sigma weight residual 180.00 120.17 59.83 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA PRO C 421 " pdb=" C PRO C 421 " pdb=" N ALA C 422 " pdb=" CA ALA C 422 " ideal model delta harmonic sigma weight residual -180.00 -123.35 -56.65 0 5.00e+00 4.00e-02 1.28e+02 ... (remaining 19980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 4605 0.131 - 0.262: 167 0.262 - 0.393: 27 0.393 - 0.523: 8 0.523 - 0.654: 3 Chirality restraints: 4810 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 378 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C1 NAG A1009 " pdb=" ND2 ASN A 412 " pdb=" C2 NAG A1009 " pdb=" O5 NAG A1009 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 378 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.12e+00 ... (remaining 4807 not shown) Planarity restraints: 5291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 660 " 0.036 2.00e-02 2.50e+03 7.08e-02 5.01e+01 pdb=" C THR A 660 " -0.122 2.00e-02 2.50e+03 pdb=" O THR A 660 " 0.045 2.00e-02 2.50e+03 pdb=" N VAL A 661 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 660 " 0.031 2.00e-02 2.50e+03 6.44e-02 4.15e+01 pdb=" C THR B 660 " -0.111 2.00e-02 2.50e+03 pdb=" O THR B 660 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL B 661 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 422 " -0.029 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C ALA C 422 " 0.103 2.00e-02 2.50e+03 pdb=" O ALA C 422 " -0.039 2.00e-02 2.50e+03 pdb=" N ASN C 423 " -0.034 2.00e-02 2.50e+03 ... (remaining 5288 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7802 2.79 - 3.32: 26852 3.32 - 3.84: 48963 3.84 - 4.37: 59027 4.37 - 4.90: 100656 Nonbonded interactions: 243300 Sorted by model distance: nonbonded pdb=" O ALA E 58 " pdb=" OH TYR E 74 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.270 3.040 nonbonded pdb=" O THR D 730 " pdb=" O2 BMA O 3 " model vdw 2.276 3.040 nonbonded pdb=" NH2 ARG A 634 " pdb=" OE2 GLU B 625 " model vdw 2.290 3.120 nonbonded pdb=" OG SER B 585 " pdb=" OE1 GLU C 841 " model vdw 2.292 3.040 ... (remaining 243295 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)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 864)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 864)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 864)) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' } 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 35.090 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.011 0.136 31730 Z= 0.481 Angle : 1.504 29.023 42902 Z= 0.760 Chirality : 0.067 0.654 4810 Planarity : 0.008 0.071 5262 Dihedral : 19.394 171.582 13038 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.20 % Favored : 89.44 % Rotamer: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.88 % 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: -5.74 (0.10), residues: 3679 helix: -4.39 (0.06), residues: 1439 sheet: -3.90 (0.19), residues: 474 loop : -3.18 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 58 TYR 0.038 0.004 TYR A 488 PHE 0.044 0.003 PHE C 735 TRP 0.080 0.005 TRP C 613 HIS 0.019 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.01065 (31658) covalent geometry : angle 1.44699 (42701) SS BOND : bond 0.00414 ( 15) SS BOND : angle 1.13181 ( 30) hydrogen bonds : bond 0.29134 ( 949) hydrogen bonds : angle 10.12134 ( 2762) link_ALPHA1-3 : bond 0.01139 ( 4) link_ALPHA1-3 : angle 4.23163 ( 12) link_ALPHA1-6 : bond 0.00582 ( 4) link_ALPHA1-6 : angle 1.84967 ( 12) link_BETA1-3 : bond 0.00926 ( 3) link_BETA1-3 : angle 5.16870 ( 9) link_BETA1-4 : bond 0.01799 ( 17) link_BETA1-4 : angle 4.29722 ( 51) link_NAG-ASN : bond 0.01609 ( 29) link_NAG-ASN : angle 8.45561 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 749 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 LEU cc_start: 0.9143 (mt) cc_final: 0.8816 (mt) REVERT: A 460 GLU cc_start: 0.7772 (pt0) cc_final: 0.7569 (tp30) REVERT: A 487 LYS cc_start: 0.7924 (mttm) cc_final: 0.7648 (mtpt) REVERT: A 501 MET cc_start: 0.5080 (mtm) cc_final: 0.4789 (mtp) REVERT: A 540 ILE cc_start: 0.7236 (mp) cc_final: 0.6997 (mt) REVERT: A 572 LEU cc_start: 0.8448 (mt) cc_final: 0.8080 (mp) REVERT: B 44 TYR cc_start: 0.8394 (t80) cc_final: 0.8157 (t80) REVERT: B 315 PHE cc_start: 0.7204 (m-10) cc_final: 0.7001 (m-10) REVERT: B 477 THR cc_start: 0.8460 (p) cc_final: 0.8242 (t) REVERT: B 669 ASP cc_start: 0.7637 (t70) cc_final: 0.7012 (t0) REVERT: B 762 LYS cc_start: 0.8329 (mtpt) cc_final: 0.8031 (mtmm) REVERT: B 790 LYS cc_start: 0.8349 (mttm) cc_final: 0.7960 (mtmt) REVERT: B 794 MET cc_start: 0.8754 (mtm) cc_final: 0.8544 (mtp) REVERT: C 86 TYR cc_start: 0.7854 (m-80) cc_final: 0.7415 (m-80) REVERT: C 260 ASP cc_start: 0.6809 (m-30) cc_final: 0.6592 (m-30) REVERT: C 482 LEU cc_start: 0.8270 (mt) cc_final: 0.7927 (mp) REVERT: C 669 ASP cc_start: 0.7927 (t70) cc_final: 0.7578 (t0) REVERT: C 770 MET cc_start: 0.8038 (tpt) cc_final: 0.7647 (tpt) REVERT: D 337 PHE cc_start: 0.8125 (t80) cc_final: 0.7015 (t80) REVERT: D 439 LEU cc_start: 0.7279 (pt) cc_final: 0.6962 (tt) REVERT: D 713 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7390 (ttm-80) REVERT: E 74 TYR cc_start: 0.8036 (m-80) cc_final: 0.7830 (m-80) REVERT: E 138 TRP cc_start: 0.8375 (t60) cc_final: 0.8108 (t60) REVERT: E 342 GLN cc_start: 0.5517 (pt0) cc_final: 0.5260 (pp30) outliers start: 2 outliers final: 1 residues processed: 751 average time/residue: 0.2330 time to fit residues: 265.4488 Evaluate side-chains 413 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 141 ASN A 196 ASN A 286 ASN A 288 GLN A 348 ASN A 381 ASN A 456 ASN A 596 ASN A 604 ASN A 610 ASN A 849 ASN B 141 ASN B 196 ASN B 286 ASN B 350 HIS B 367 HIS B 381 ASN B 456 ASN B 596 ASN B 604 ASN B 610 ASN B 621 GLN B 792 HIS C 141 ASN C 196 ASN C 286 ASN C 288 GLN C 348 ASN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN C 456 ASN C 596 ASN C 610 ASN D 123 ASN D 141 ASN D 196 ASN D 286 ASN D 348 ASN D 381 ASN D 423 ASN D 456 ASN D 549 ASN D 596 ASN D 604 ASN D 610 ASN D 621 GLN ** D 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 82 GLN E 203 GLN E 317 ASN E 342 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.181345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139966 restraints weight = 58456.963| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.54 r_work: 0.3337 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31730 Z= 0.166 Angle : 0.865 20.287 42902 Z= 0.409 Chirality : 0.050 0.432 4810 Planarity : 0.006 0.056 5262 Dihedral : 21.036 176.445 6008 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.39 % Favored : 90.42 % Rotamer: Outliers : 1.96 % Allowed : 9.79 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.51 % 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: -4.13 (0.12), residues: 3679 helix: -2.39 (0.10), residues: 1492 sheet: -3.56 (0.20), residues: 479 loop : -2.72 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 748 TYR 0.022 0.002 TYR A 44 PHE 0.044 0.002 PHE B 337 TRP 0.024 0.002 TRP C 353 HIS 0.010 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00368 (31658) covalent geometry : angle 0.82076 (42701) SS BOND : bond 0.00518 ( 15) SS BOND : angle 1.01930 ( 30) hydrogen bonds : bond 0.04949 ( 949) hydrogen bonds : angle 5.00839 ( 2762) link_ALPHA1-3 : bond 0.02004 ( 4) link_ALPHA1-3 : angle 2.75767 ( 12) link_ALPHA1-6 : bond 0.00917 ( 4) link_ALPHA1-6 : angle 3.10818 ( 12) link_BETA1-3 : bond 0.00747 ( 3) link_BETA1-3 : angle 5.98061 ( 9) link_BETA1-4 : bond 0.01237 ( 17) link_BETA1-4 : angle 2.89574 ( 51) link_NAG-ASN : bond 0.00980 ( 29) link_NAG-ASN : angle 5.15690 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 456 time to evaluate : 1.770 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 212 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8161 (mtmm) REVERT: A 233 GLU cc_start: 0.7986 (mp0) cc_final: 0.7666 (mp0) REVERT: A 467 LEU cc_start: 0.7991 (mt) cc_final: 0.7773 (mt) REVERT: A 487 LYS cc_start: 0.8063 (mttm) cc_final: 0.7848 (mtpt) REVERT: A 501 MET cc_start: 0.5392 (mtm) cc_final: 0.4535 (mtt) REVERT: A 543 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6417 (ttm170) REVERT: A 668 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6756 (pp) REVERT: A 705 MET cc_start: 0.7603 (mtp) cc_final: 0.6963 (mtp) REVERT: A 755 ILE cc_start: 0.8520 (mm) cc_final: 0.8247 (mt) REVERT: B 166 PHE cc_start: 0.8802 (t80) cc_final: 0.8549 (t80) REVERT: B 292 ILE cc_start: 0.9059 (mm) cc_final: 0.8707 (mt) REVERT: B 531 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8547 (mmtp) REVERT: B 669 ASP cc_start: 0.8126 (t70) cc_final: 0.7391 (t0) REVERT: C 86 TYR cc_start: 0.7741 (m-80) cc_final: 0.7310 (m-80) REVERT: C 198 ARG cc_start: 0.7733 (tpt-90) cc_final: 0.7495 (mmm160) REVERT: C 200 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8082 (tttt) REVERT: C 260 ASP cc_start: 0.7237 (m-30) cc_final: 0.6997 (m-30) REVERT: C 298 MET cc_start: 0.8757 (mmp) cc_final: 0.8499 (mmp) REVERT: C 482 LEU cc_start: 0.8504 (mt) cc_final: 0.8168 (mp) REVERT: C 531 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.7857 (tttt) REVERT: C 613 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7295 (t60) REVERT: C 629 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8077 (ptpp) REVERT: C 669 ASP cc_start: 0.8094 (t70) cc_final: 0.7712 (t0) REVERT: C 691 MET cc_start: 0.7732 (ttp) cc_final: 0.7328 (tmm) REVERT: C 770 MET cc_start: 0.8093 (tpt) cc_final: 0.7663 (tpt) REVERT: D 50 MET cc_start: 0.7522 (mtp) cc_final: 0.7069 (mtp) REVERT: D 140 ASP cc_start: 0.7178 (t0) cc_final: 0.6828 (t0) REVERT: D 141 ASN cc_start: 0.9110 (t0) cc_final: 0.8781 (t0) REVERT: D 222 LYS cc_start: 0.9006 (mptm) cc_final: 0.8703 (mmmt) REVERT: D 337 PHE cc_start: 0.8039 (t80) cc_final: 0.7700 (t80) REVERT: D 556 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8671 (mp) REVERT: D 568 LEU cc_start: 0.8585 (mt) cc_final: 0.8314 (mt) REVERT: D 713 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7516 (ttm-80) REVERT: D 871 CYS cc_start: 0.7726 (p) cc_final: 0.6851 (p) REVERT: D 873 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6953 (ptt-90) REVERT: E 62 TYR cc_start: 0.7889 (t80) cc_final: 0.7477 (t80) REVERT: E 138 TRP cc_start: 0.8190 (t60) cc_final: 0.7881 (t60) REVERT: E 192 GLN cc_start: 0.8154 (mm110) cc_final: 0.7742 (mm-40) REVERT: E 342 GLN cc_start: 0.5745 (pt0) cc_final: 0.5119 (pp30) outliers start: 62 outliers final: 25 residues processed: 492 average time/residue: 0.1944 time to fit residues: 152.0819 Evaluate side-chains 412 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 379 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 613 TRP Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 873 ARG Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 308 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 288 GLN A 381 ASN B 350 HIS B 381 ASN C 129 HIS ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 ASN ** D 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.172366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116975 restraints weight = 75181.162| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 4.53 r_work: 0.3166 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31730 Z= 0.169 Angle : 0.804 19.433 42902 Z= 0.375 Chirality : 0.049 0.434 4810 Planarity : 0.005 0.061 5262 Dihedral : 18.462 164.696 6008 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.58 % Favored : 90.31 % Rotamer: Outliers : 1.87 % Allowed : 10.04 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.25 % 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: -3.10 (0.13), residues: 3679 helix: -1.10 (0.12), residues: 1493 sheet: -3.45 (0.21), residues: 482 loop : -2.46 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 481 TYR 0.021 0.002 TYR A 44 PHE 0.038 0.002 PHE B 337 TRP 0.027 0.002 TRP D 296 HIS 0.005 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00391 (31658) covalent geometry : angle 0.76308 (42701) SS BOND : bond 0.01168 ( 15) SS BOND : angle 1.57267 ( 30) hydrogen bonds : bond 0.04094 ( 949) hydrogen bonds : angle 4.46848 ( 2762) link_ALPHA1-3 : bond 0.01810 ( 4) link_ALPHA1-3 : angle 3.32468 ( 12) link_ALPHA1-6 : bond 0.01304 ( 4) link_ALPHA1-6 : angle 2.73200 ( 12) link_BETA1-3 : bond 0.00612 ( 3) link_BETA1-3 : angle 5.82585 ( 9) link_BETA1-4 : bond 0.01050 ( 17) link_BETA1-4 : angle 2.78404 ( 51) link_NAG-ASN : bond 0.00899 ( 29) link_NAG-ASN : angle 4.63617 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 398 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6504 (ttp) REVERT: A 152 ASP cc_start: 0.8672 (t0) cc_final: 0.8434 (t0) REVERT: A 212 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8102 (mtmm) REVERT: A 248 MET cc_start: 0.8534 (mmm) cc_final: 0.7981 (mmm) REVERT: A 336 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: A 487 LYS cc_start: 0.7876 (mttm) cc_final: 0.7552 (mtpt) REVERT: A 501 MET cc_start: 0.5060 (mtm) cc_final: 0.4241 (mtt) REVERT: A 538 ILE cc_start: 0.8541 (mt) cc_final: 0.8111 (pt) REVERT: A 540 ILE cc_start: 0.7174 (mp) cc_final: 0.6967 (mt) REVERT: A 664 MET cc_start: 0.6899 (mmm) cc_final: 0.6657 (mmm) REVERT: A 668 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6567 (pp) REVERT: A 749 ASN cc_start: 0.8124 (m-40) cc_final: 0.7812 (t0) REVERT: A 755 ILE cc_start: 0.8293 (mm) cc_final: 0.8080 (mt) REVERT: B 292 ILE cc_start: 0.8901 (mm) cc_final: 0.8621 (mt) REVERT: B 337 PHE cc_start: 0.8078 (t80) cc_final: 0.7848 (t80) REVERT: B 627 MET cc_start: 0.8923 (mmm) cc_final: 0.8502 (mmm) REVERT: B 669 ASP cc_start: 0.8189 (t70) cc_final: 0.7521 (t0) REVERT: B 673 ASP cc_start: 0.8436 (m-30) cc_final: 0.7866 (m-30) REVERT: B 790 LYS cc_start: 0.8063 (mttm) cc_final: 0.7785 (mtmt) REVERT: C 55 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7874 (tm) REVERT: C 86 TYR cc_start: 0.7893 (m-80) cc_final: 0.7272 (m-80) REVERT: C 198 ARG cc_start: 0.7684 (tpt-90) cc_final: 0.7286 (mmm160) REVERT: C 212 LYS cc_start: 0.8654 (mttp) cc_final: 0.8273 (mtmm) REVERT: C 298 MET cc_start: 0.9045 (mmp) cc_final: 0.8761 (mmp) REVERT: C 482 LEU cc_start: 0.8605 (mt) cc_final: 0.8236 (mp) REVERT: C 531 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8063 (mmtp) REVERT: C 604 ASN cc_start: 0.8511 (t0) cc_final: 0.8250 (t0) REVERT: C 613 TRP cc_start: 0.7754 (OUTLIER) cc_final: 0.6684 (t60) REVERT: C 629 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7548 (ptpp) REVERT: C 669 ASP cc_start: 0.8369 (t70) cc_final: 0.7982 (t0) REVERT: C 691 MET cc_start: 0.7660 (ttp) cc_final: 0.7271 (tmm) REVERT: C 770 MET cc_start: 0.8106 (tpt) cc_final: 0.7619 (tpt) REVERT: D 140 ASP cc_start: 0.7509 (t0) cc_final: 0.6958 (t0) REVERT: D 141 ASN cc_start: 0.9099 (t0) cc_final: 0.8710 (t0) REVERT: D 222 LYS cc_start: 0.9184 (mptm) cc_final: 0.8555 (mmmt) REVERT: D 337 PHE cc_start: 0.8101 (t80) cc_final: 0.7290 (t80) REVERT: D 340 MET cc_start: 0.7013 (tpp) cc_final: 0.6275 (mpp) REVERT: D 556 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8515 (mp) REVERT: D 572 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7452 (mm) REVERT: D 713 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7156 (ttm-80) REVERT: D 800 ARG cc_start: 0.8539 (tpt170) cc_final: 0.8076 (tpt90) REVERT: D 873 ARG cc_start: 0.7576 (ptt-90) cc_final: 0.7292 (ptt-90) REVERT: E 101 ARG cc_start: 0.9084 (mtm110) cc_final: 0.8492 (mtm-85) REVERT: E 121 TYR cc_start: 0.7895 (m-80) cc_final: 0.7639 (m-80) REVERT: E 138 TRP cc_start: 0.7846 (t60) cc_final: 0.7623 (t60) REVERT: E 178 GLN cc_start: 0.8356 (mp10) cc_final: 0.7806 (mp10) REVERT: E 342 GLN cc_start: 0.5467 (pt0) cc_final: 0.4923 (pp30) outliers start: 59 outliers final: 27 residues processed: 440 average time/residue: 0.1821 time to fit residues: 130.9748 Evaluate side-chains 397 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 361 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 613 TRP Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 595 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 223 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 273 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 363 optimal weight: 0.0070 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 350 HIS ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 ASN E 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.171707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115752 restraints weight = 63606.090| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.12 r_work: 0.3176 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31730 Z= 0.165 Angle : 0.773 19.048 42902 Z= 0.359 Chirality : 0.048 0.419 4810 Planarity : 0.004 0.062 5262 Dihedral : 17.054 150.004 6008 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.71 % Favored : 90.26 % Rotamer: Outliers : 1.77 % Allowed : 11.47 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.53 (0.14), residues: 3679 helix: -0.41 (0.13), residues: 1488 sheet: -3.27 (0.21), residues: 480 loop : -2.34 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 349 TYR 0.032 0.002 TYR E 74 PHE 0.035 0.002 PHE B 337 TRP 0.023 0.002 TRP D 589 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00387 (31658) covalent geometry : angle 0.73493 (42701) SS BOND : bond 0.00432 ( 15) SS BOND : angle 0.77403 ( 30) hydrogen bonds : bond 0.03617 ( 949) hydrogen bonds : angle 4.28192 ( 2762) link_ALPHA1-3 : bond 0.01954 ( 4) link_ALPHA1-3 : angle 3.07936 ( 12) link_ALPHA1-6 : bond 0.01186 ( 4) link_ALPHA1-6 : angle 2.17343 ( 12) link_BETA1-3 : bond 0.00579 ( 3) link_BETA1-3 : angle 5.80725 ( 9) link_BETA1-4 : bond 0.01017 ( 17) link_BETA1-4 : angle 2.73478 ( 51) link_NAG-ASN : bond 0.00838 ( 29) link_NAG-ASN : angle 4.42104 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 381 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6322 (ttp) REVERT: A 152 ASP cc_start: 0.8667 (t0) cc_final: 0.8454 (t0) REVERT: A 212 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8175 (mtmm) REVERT: A 248 MET cc_start: 0.8566 (mmm) cc_final: 0.8114 (mmm) REVERT: A 316 MET cc_start: 0.8853 (ttm) cc_final: 0.8642 (ttm) REVERT: A 336 GLN cc_start: 0.7451 (mt0) cc_final: 0.6968 (mp10) REVERT: A 487 LYS cc_start: 0.7750 (mttm) cc_final: 0.7374 (mtpt) REVERT: A 501 MET cc_start: 0.5153 (mtm) cc_final: 0.4858 (mtp) REVERT: A 538 ILE cc_start: 0.8524 (mt) cc_final: 0.8214 (pt) REVERT: A 668 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6461 (pp) REVERT: A 749 ASN cc_start: 0.8217 (m-40) cc_final: 0.7913 (t0) REVERT: A 770 MET cc_start: 0.7662 (tpt) cc_final: 0.6909 (tpt) REVERT: A 818 GLN cc_start: 0.7947 (pt0) cc_final: 0.7642 (pm20) REVERT: B 292 ILE cc_start: 0.8898 (mm) cc_final: 0.8625 (mt) REVERT: B 627 MET cc_start: 0.8908 (mmm) cc_final: 0.8386 (mmm) REVERT: B 665 GLU cc_start: 0.7508 (mp0) cc_final: 0.7231 (mp0) REVERT: B 790 LYS cc_start: 0.8155 (mttm) cc_final: 0.7860 (mtmt) REVERT: C 43 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 54 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 55 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7979 (tp) REVERT: C 86 TYR cc_start: 0.7900 (m-80) cc_final: 0.7366 (m-80) REVERT: C 198 ARG cc_start: 0.7687 (tpt-90) cc_final: 0.7304 (mmm160) REVERT: C 200 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7847 (tttt) REVERT: C 212 LYS cc_start: 0.8666 (mttp) cc_final: 0.8330 (mtmm) REVERT: C 247 MET cc_start: 0.8784 (mmm) cc_final: 0.8538 (mmt) REVERT: C 298 MET cc_start: 0.9081 (mmp) cc_final: 0.8801 (mmp) REVERT: C 531 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8086 (mmtp) REVERT: C 604 ASN cc_start: 0.8601 (t0) cc_final: 0.8383 (t0) REVERT: C 613 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6304 (t60) REVERT: C 629 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7552 (ptpp) REVERT: C 669 ASP cc_start: 0.8274 (t70) cc_final: 0.7904 (t0) REVERT: C 691 MET cc_start: 0.7656 (ttp) cc_final: 0.6853 (tmm) REVERT: C 770 MET cc_start: 0.8118 (tpt) cc_final: 0.7664 (tpt) REVERT: D 140 ASP cc_start: 0.7623 (t0) cc_final: 0.7068 (t0) REVERT: D 141 ASN cc_start: 0.9143 (t0) cc_final: 0.8817 (t0) REVERT: D 323 MET cc_start: 0.8789 (mmm) cc_final: 0.8588 (tpp) REVERT: D 337 PHE cc_start: 0.8138 (t80) cc_final: 0.7417 (t80) REVERT: D 340 MET cc_start: 0.7107 (tpp) cc_final: 0.6396 (mpp) REVERT: D 556 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8521 (mp) REVERT: D 572 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7491 (mm) REVERT: D 713 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7155 (ttm-80) REVERT: D 800 ARG cc_start: 0.8515 (tpt170) cc_final: 0.8001 (tpt90) REVERT: E 101 ARG cc_start: 0.9044 (mtm110) cc_final: 0.8425 (mtm-85) REVERT: E 178 GLN cc_start: 0.8304 (mp10) cc_final: 0.7737 (mp10) REVERT: E 195 GLN cc_start: 0.8066 (pt0) cc_final: 0.7592 (pp30) REVERT: E 342 GLN cc_start: 0.5380 (pt0) cc_final: 0.4840 (pp30) outliers start: 56 outliers final: 34 residues processed: 422 average time/residue: 0.1893 time to fit residues: 129.5523 Evaluate side-chains 401 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 358 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 613 TRP Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 70 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 97 optimal weight: 0.2980 chunk 248 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 312 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 849 ASN B 129 HIS B 328 HIS B 350 HIS B 381 ASN B 621 GLN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS E 56 HIS E 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118650 restraints weight = 53693.360| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.61 r_work: 0.3222 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31730 Z= 0.132 Angle : 0.725 18.534 42902 Z= 0.337 Chirality : 0.046 0.420 4810 Planarity : 0.004 0.062 5262 Dihedral : 15.754 150.896 6008 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.73 % Favored : 91.21 % Rotamer: Outliers : 1.77 % Allowed : 12.31 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.00 (0.14), residues: 3679 helix: 0.16 (0.14), residues: 1488 sheet: -3.00 (0.22), residues: 476 loop : -2.18 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 349 TYR 0.028 0.001 TYR E 74 PHE 0.039 0.001 PHE B 337 TRP 0.030 0.002 TRP E 138 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00300 (31658) covalent geometry : angle 0.68830 (42701) SS BOND : bond 0.00340 ( 15) SS BOND : angle 0.74463 ( 30) hydrogen bonds : bond 0.03298 ( 949) hydrogen bonds : angle 4.09440 ( 2762) link_ALPHA1-3 : bond 0.01918 ( 4) link_ALPHA1-3 : angle 2.56371 ( 12) link_ALPHA1-6 : bond 0.00860 ( 4) link_ALPHA1-6 : angle 1.43511 ( 12) link_BETA1-3 : bond 0.00602 ( 3) link_BETA1-3 : angle 5.63835 ( 9) link_BETA1-4 : bond 0.00928 ( 17) link_BETA1-4 : angle 2.64944 ( 51) link_NAG-ASN : bond 0.00884 ( 29) link_NAG-ASN : angle 4.23045 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 390 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.8619 (t0) cc_final: 0.8331 (t0) REVERT: A 212 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8272 (mtmm) REVERT: A 316 MET cc_start: 0.8866 (ttm) cc_final: 0.8593 (ttm) REVERT: A 335 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 336 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: A 487 LYS cc_start: 0.7795 (mttm) cc_final: 0.7549 (mtpt) REVERT: A 501 MET cc_start: 0.5223 (mtm) cc_final: 0.4712 (mtt) REVERT: A 538 ILE cc_start: 0.8565 (mt) cc_final: 0.8300 (pt) REVERT: A 543 ARG cc_start: 0.7149 (mtp85) cc_final: 0.6009 (ttm110) REVERT: A 668 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6417 (pp) REVERT: A 709 MET cc_start: 0.5714 (mtp) cc_final: 0.5512 (mtp) REVERT: A 744 PHE cc_start: 0.8072 (t80) cc_final: 0.7695 (t80) REVERT: A 749 ASN cc_start: 0.8333 (m-40) cc_final: 0.8031 (t0) REVERT: A 800 ARG cc_start: 0.7802 (tpt170) cc_final: 0.7132 (tpt90) REVERT: A 818 GLN cc_start: 0.7945 (pt0) cc_final: 0.7622 (pm20) REVERT: B 292 ILE cc_start: 0.8826 (mm) cc_final: 0.8582 (mt) REVERT: B 443 TYR cc_start: 0.8355 (m-80) cc_final: 0.8143 (m-80) REVERT: B 625 GLU cc_start: 0.6692 (pt0) cc_final: 0.6289 (pm20) REVERT: B 627 MET cc_start: 0.8853 (mmm) cc_final: 0.8480 (mmm) REVERT: B 738 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: B 790 LYS cc_start: 0.8133 (mttm) cc_final: 0.7821 (mtmt) REVERT: B 800 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7507 (mmp80) REVERT: C 43 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7470 (tm-30) REVERT: C 54 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7830 (tp30) REVERT: C 86 TYR cc_start: 0.7890 (m-80) cc_final: 0.7138 (m-80) REVERT: C 198 ARG cc_start: 0.7595 (tpt-90) cc_final: 0.7209 (mmm160) REVERT: C 200 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7763 (tttt) REVERT: C 212 LYS cc_start: 0.8685 (mttp) cc_final: 0.8355 (mtmm) REVERT: C 298 MET cc_start: 0.9039 (mmp) cc_final: 0.8769 (mmp) REVERT: C 315 PHE cc_start: 0.6599 (m-80) cc_final: 0.6267 (m-80) REVERT: C 482 LEU cc_start: 0.8501 (mt) cc_final: 0.7367 (mp) REVERT: C 604 ASN cc_start: 0.8621 (t0) cc_final: 0.8156 (t0) REVERT: C 613 TRP cc_start: 0.7696 (OUTLIER) cc_final: 0.6167 (t60) REVERT: C 629 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7701 (ptpp) REVERT: C 669 ASP cc_start: 0.8314 (t70) cc_final: 0.7911 (t0) REVERT: C 691 MET cc_start: 0.7662 (ttp) cc_final: 0.6838 (tmm) REVERT: C 770 MET cc_start: 0.8039 (tpt) cc_final: 0.7548 (tpt) REVERT: D 140 ASP cc_start: 0.7573 (t0) cc_final: 0.7233 (t70) REVERT: D 141 ASN cc_start: 0.9123 (t0) cc_final: 0.8854 (t0) REVERT: D 337 PHE cc_start: 0.8157 (t80) cc_final: 0.7441 (t80) REVERT: D 340 MET cc_start: 0.7072 (tpp) cc_final: 0.6397 (mpp) REVERT: D 572 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7210 (mm) REVERT: D 713 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7084 (ttm-80) REVERT: D 800 ARG cc_start: 0.8487 (tpt170) cc_final: 0.7991 (tpt90) REVERT: E 101 ARG cc_start: 0.9035 (mtm110) cc_final: 0.8418 (mtm-85) REVERT: E 178 GLN cc_start: 0.8266 (mp10) cc_final: 0.7689 (mp10) REVERT: E 342 GLN cc_start: 0.5304 (pt0) cc_final: 0.4792 (pp30) outliers start: 56 outliers final: 27 residues processed: 427 average time/residue: 0.1882 time to fit residues: 130.0927 Evaluate side-chains 397 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 363 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 613 TRP Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 595 CYS Chi-restraints excluded: chain D residue 761 SER Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 275 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 GLN C 381 ASN D 605 ASN E 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.172278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117677 restraints weight = 61341.321| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.76 r_work: 0.3198 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31730 Z= 0.146 Angle : 0.714 18.314 42902 Z= 0.332 Chirality : 0.046 0.429 4810 Planarity : 0.004 0.062 5262 Dihedral : 15.191 151.826 6008 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.25 % Favored : 90.72 % Rotamer: Outliers : 1.59 % Allowed : 12.62 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.78 (0.14), residues: 3679 helix: 0.39 (0.14), residues: 1485 sheet: -2.86 (0.23), residues: 462 loop : -2.13 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 431 TYR 0.027 0.001 TYR E 74 PHE 0.036 0.001 PHE B 337 TRP 0.043 0.002 TRP E 138 HIS 0.021 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00342 (31658) covalent geometry : angle 0.67828 (42701) SS BOND : bond 0.00302 ( 15) SS BOND : angle 0.65651 ( 30) hydrogen bonds : bond 0.03257 ( 949) hydrogen bonds : angle 4.02796 ( 2762) link_ALPHA1-3 : bond 0.01935 ( 4) link_ALPHA1-3 : angle 2.55150 ( 12) link_ALPHA1-6 : bond 0.00693 ( 4) link_ALPHA1-6 : angle 1.51093 ( 12) link_BETA1-3 : bond 0.00603 ( 3) link_BETA1-3 : angle 5.55951 ( 9) link_BETA1-4 : bond 0.00883 ( 17) link_BETA1-4 : angle 2.49420 ( 51) link_NAG-ASN : bond 0.00848 ( 29) link_NAG-ASN : angle 4.16199 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 371 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6708 (ttp) REVERT: A 152 ASP cc_start: 0.8637 (t0) cc_final: 0.8352 (t0) REVERT: A 212 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8270 (mtmm) REVERT: A 294 GLU cc_start: 0.8046 (pp20) cc_final: 0.7788 (pp20) REVERT: A 316 MET cc_start: 0.8875 (ttm) cc_final: 0.8628 (ttm) REVERT: A 487 LYS cc_start: 0.7820 (mttm) cc_final: 0.7605 (mtmm) REVERT: A 501 MET cc_start: 0.5183 (mtm) cc_final: 0.4677 (mtt) REVERT: A 538 ILE cc_start: 0.8579 (mt) cc_final: 0.8304 (pt) REVERT: A 664 MET cc_start: 0.6463 (mtp) cc_final: 0.6165 (mtp) REVERT: A 668 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6378 (pp) REVERT: A 712 ARG cc_start: 0.7078 (mtt90) cc_final: 0.6745 (mtt90) REVERT: A 749 ASN cc_start: 0.8356 (m-40) cc_final: 0.8056 (t0) REVERT: A 770 MET cc_start: 0.7792 (tpt) cc_final: 0.6717 (tpt) REVERT: A 818 GLN cc_start: 0.8011 (pt0) cc_final: 0.7675 (pm20) REVERT: B 248 MET cc_start: 0.8663 (mmt) cc_final: 0.8416 (mmt) REVERT: B 292 ILE cc_start: 0.8846 (mm) cc_final: 0.8612 (mt) REVERT: B 443 TYR cc_start: 0.8451 (m-80) cc_final: 0.8213 (m-80) REVERT: B 625 GLU cc_start: 0.6716 (pt0) cc_final: 0.6361 (pm20) REVERT: B 738 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8462 (mm-30) REVERT: B 790 LYS cc_start: 0.8202 (mttm) cc_final: 0.7952 (mtmt) REVERT: C 43 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7470 (tm-30) REVERT: C 54 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7869 (tp30) REVERT: C 198 ARG cc_start: 0.7670 (tpt-90) cc_final: 0.7309 (mmm160) REVERT: C 200 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7799 (tttt) REVERT: C 212 LYS cc_start: 0.8691 (mttp) cc_final: 0.8375 (mtmm) REVERT: C 298 MET cc_start: 0.9079 (mmp) cc_final: 0.8803 (mmp) REVERT: C 315 PHE cc_start: 0.6719 (m-80) cc_final: 0.6322 (m-80) REVERT: C 531 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8192 (mmtp) REVERT: C 604 ASN cc_start: 0.8676 (t0) cc_final: 0.8221 (t0) REVERT: C 629 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7709 (ptpp) REVERT: C 669 ASP cc_start: 0.8330 (t70) cc_final: 0.7920 (t0) REVERT: C 691 MET cc_start: 0.7712 (ttp) cc_final: 0.6885 (tmm) REVERT: C 761 SER cc_start: 0.9014 (t) cc_final: 0.8482 (m) REVERT: C 770 MET cc_start: 0.8139 (tpt) cc_final: 0.7668 (tpt) REVERT: D 141 ASN cc_start: 0.9122 (t0) cc_final: 0.8858 (t0) REVERT: D 337 PHE cc_start: 0.8197 (t80) cc_final: 0.7549 (t80) REVERT: D 340 MET cc_start: 0.7121 (tpp) cc_final: 0.6567 (mpp) REVERT: D 572 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7357 (mm) REVERT: D 713 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7085 (ttm-80) REVERT: D 800 ARG cc_start: 0.8519 (tpt170) cc_final: 0.7991 (tpt90) REVERT: E 95 GLU cc_start: 0.7418 (tp30) cc_final: 0.7002 (mm-30) REVERT: E 101 ARG cc_start: 0.8999 (mtm110) cc_final: 0.8413 (mtm-85) REVERT: E 178 GLN cc_start: 0.8264 (mp10) cc_final: 0.7677 (mp10) REVERT: E 195 GLN cc_start: 0.7957 (pt0) cc_final: 0.7581 (pp30) REVERT: E 308 MET cc_start: 0.7259 (mmt) cc_final: 0.7003 (mmp) REVERT: E 342 GLN cc_start: 0.5343 (pt0) cc_final: 0.4977 (pp30) outliers start: 50 outliers final: 33 residues processed: 407 average time/residue: 0.1889 time to fit residues: 124.0173 Evaluate side-chains 396 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 356 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 595 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 761 SER Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 167 optimal weight: 10.0000 chunk 329 optimal weight: 0.0770 chunk 168 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 348 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 153 optimal weight: 0.8980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 381 ASN E 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142164 restraints weight = 66531.382| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.28 r_work: 0.3259 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31730 Z= 0.135 Angle : 0.705 17.986 42902 Z= 0.329 Chirality : 0.046 0.429 4810 Planarity : 0.004 0.060 5262 Dihedral : 14.708 151.897 6008 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.73 % Favored : 91.24 % Rotamer: Outliers : 1.55 % Allowed : 12.96 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.56 (0.14), residues: 3679 helix: 0.61 (0.14), residues: 1484 sheet: -2.70 (0.24), residues: 452 loop : -2.05 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 431 TYR 0.027 0.001 TYR C 86 PHE 0.039 0.001 PHE B 337 TRP 0.025 0.001 TRP E 138 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00313 (31658) covalent geometry : angle 0.67143 (42701) SS BOND : bond 0.00368 ( 15) SS BOND : angle 0.56166 ( 30) hydrogen bonds : bond 0.03182 ( 949) hydrogen bonds : angle 3.97846 ( 2762) link_ALPHA1-3 : bond 0.01820 ( 4) link_ALPHA1-3 : angle 2.47014 ( 12) link_ALPHA1-6 : bond 0.00661 ( 4) link_ALPHA1-6 : angle 1.43905 ( 12) link_BETA1-3 : bond 0.00564 ( 3) link_BETA1-3 : angle 5.39437 ( 9) link_BETA1-4 : bond 0.00910 ( 17) link_BETA1-4 : angle 2.27057 ( 51) link_NAG-ASN : bond 0.00870 ( 29) link_NAG-ASN : angle 4.08646 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 377 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.5623 (mtm) cc_final: 0.4779 (mtt) REVERT: A 543 ARG cc_start: 0.7295 (mtp85) cc_final: 0.6490 (ttm110) REVERT: A 664 MET cc_start: 0.6692 (mtp) cc_final: 0.6451 (mtp) REVERT: A 668 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6614 (pp) REVERT: A 770 MET cc_start: 0.7422 (tpt) cc_final: 0.6279 (tpt) REVERT: A 800 ARG cc_start: 0.7797 (tpt170) cc_final: 0.7459 (tpt90) REVERT: B 64 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8634 (mp) REVERT: B 292 ILE cc_start: 0.9046 (mm) cc_final: 0.8716 (mt) REVERT: B 443 TYR cc_start: 0.8793 (m-80) cc_final: 0.8580 (m-80) REVERT: B 796 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 54 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7927 (tp30) REVERT: C 86 TYR cc_start: 0.7597 (m-80) cc_final: 0.6901 (m-80) REVERT: C 200 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8100 (tttt) REVERT: C 298 MET cc_start: 0.8791 (mmp) cc_final: 0.8591 (mmp) REVERT: C 315 PHE cc_start: 0.6744 (m-80) cc_final: 0.6516 (m-80) REVERT: C 531 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8423 (mmtp) REVERT: C 604 ASN cc_start: 0.8292 (t0) cc_final: 0.8009 (t0) REVERT: C 629 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8274 (ptpp) REVERT: C 669 ASP cc_start: 0.7964 (t70) cc_final: 0.7608 (t0) REVERT: C 691 MET cc_start: 0.7837 (ttp) cc_final: 0.7493 (tmm) REVERT: C 761 SER cc_start: 0.8843 (t) cc_final: 0.8583 (m) REVERT: C 770 MET cc_start: 0.8204 (tpt) cc_final: 0.7923 (tpt) REVERT: D 337 PHE cc_start: 0.8341 (t80) cc_final: 0.7799 (t80) REVERT: D 340 MET cc_start: 0.7434 (tpp) cc_final: 0.7055 (mpp) REVERT: D 498 TRP cc_start: 0.8094 (m100) cc_final: 0.7723 (m-90) REVERT: D 572 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8103 (mm) REVERT: D 626 LEU cc_start: 0.8545 (pp) cc_final: 0.8341 (pp) REVERT: D 713 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7443 (ttm-80) REVERT: D 800 ARG cc_start: 0.8420 (tpt170) cc_final: 0.8124 (tpt90) REVERT: E 62 TYR cc_start: 0.7421 (t80) cc_final: 0.6910 (t80) REVERT: E 101 ARG cc_start: 0.8688 (mtm110) cc_final: 0.8192 (mtm-85) REVERT: E 178 GLN cc_start: 0.8058 (mp10) cc_final: 0.7688 (mp10) REVERT: E 308 MET cc_start: 0.7930 (mmt) cc_final: 0.7585 (mmp) REVERT: E 342 GLN cc_start: 0.5533 (pt0) cc_final: 0.5158 (pp30) REVERT: E 381 LYS cc_start: 0.4843 (tmtt) cc_final: 0.4643 (mmtm) outliers start: 49 outliers final: 31 residues processed: 414 average time/residue: 0.1803 time to fit residues: 120.7538 Evaluate side-chains 387 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 350 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 595 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 761 SER Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 71 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 26 optimal weight: 0.0770 chunk 106 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 240 optimal weight: 0.9980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN B 129 HIS E 195 GLN ** E 203 GLN ** 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 = 0.4139 r_free = 0.4139 target = 0.178875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140247 restraints weight = 60195.690| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.26 r_work: 0.3241 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 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 = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31730 Z= 0.151 Angle : 0.714 17.822 42902 Z= 0.335 Chirality : 0.046 0.435 4810 Planarity : 0.004 0.060 5262 Dihedral : 14.462 152.394 6008 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.22 % Favored : 90.75 % Rotamer: Outliers : 1.43 % Allowed : 13.43 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.46 (0.14), residues: 3679 helix: 0.69 (0.14), residues: 1487 sheet: -2.57 (0.24), residues: 446 loop : -2.03 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 431 TYR 0.029 0.002 TYR C 86 PHE 0.036 0.001 PHE B 337 TRP 0.049 0.002 TRP E 138 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00359 (31658) covalent geometry : angle 0.68163 (42701) SS BOND : bond 0.00272 ( 15) SS BOND : angle 0.58690 ( 30) hydrogen bonds : bond 0.03221 ( 949) hydrogen bonds : angle 3.97558 ( 2762) link_ALPHA1-3 : bond 0.01758 ( 4) link_ALPHA1-3 : angle 2.52320 ( 12) link_ALPHA1-6 : bond 0.00625 ( 4) link_ALPHA1-6 : angle 1.42525 ( 12) link_BETA1-3 : bond 0.00506 ( 3) link_BETA1-3 : angle 5.24755 ( 9) link_BETA1-4 : bond 0.00793 ( 17) link_BETA1-4 : angle 2.27677 ( 51) link_NAG-ASN : bond 0.00838 ( 29) link_NAG-ASN : angle 4.02392 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 361 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.7131 (ttm) cc_final: 0.6929 (tpp) REVERT: A 501 MET cc_start: 0.5510 (mtm) cc_final: 0.4676 (mtt) REVERT: A 664 MET cc_start: 0.6703 (mtp) cc_final: 0.6353 (mtm) REVERT: A 668 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6581 (pp) REVERT: A 770 MET cc_start: 0.7518 (tpt) cc_final: 0.6402 (tpt) REVERT: A 800 ARG cc_start: 0.7820 (tpt170) cc_final: 0.7417 (tpt90) REVERT: B 64 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8632 (mp) REVERT: B 292 ILE cc_start: 0.9070 (mm) cc_final: 0.8770 (mt) REVERT: C 54 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7941 (tp30) REVERT: C 93 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8659 (mmpt) REVERT: C 200 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8112 (tttt) REVERT: C 298 MET cc_start: 0.8884 (mmp) cc_final: 0.8671 (mmp) REVERT: C 315 PHE cc_start: 0.6901 (m-80) cc_final: 0.6605 (m-80) REVERT: C 531 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8295 (mmtp) REVERT: C 604 ASN cc_start: 0.8382 (t0) cc_final: 0.8114 (t0) REVERT: C 629 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8234 (ptpp) REVERT: C 669 ASP cc_start: 0.8075 (t70) cc_final: 0.7758 (t0) REVERT: C 691 MET cc_start: 0.7865 (ttp) cc_final: 0.7483 (tmm) REVERT: C 705 MET cc_start: 0.8699 (mtp) cc_final: 0.8312 (mtt) REVERT: C 761 SER cc_start: 0.8906 (t) cc_final: 0.8620 (m) REVERT: C 770 MET cc_start: 0.8243 (tpt) cc_final: 0.7934 (tpt) REVERT: D 337 PHE cc_start: 0.8382 (t80) cc_final: 0.7817 (t80) REVERT: D 340 MET cc_start: 0.7434 (tpp) cc_final: 0.6988 (mpp) REVERT: D 498 TRP cc_start: 0.8136 (m100) cc_final: 0.7728 (m-90) REVERT: D 572 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8116 (mm) REVERT: D 800 ARG cc_start: 0.8462 (tpt170) cc_final: 0.8133 (tpt90) REVERT: E 62 TYR cc_start: 0.7556 (t80) cc_final: 0.7054 (t80) REVERT: E 101 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8256 (mtm-85) REVERT: E 178 GLN cc_start: 0.8121 (mp10) cc_final: 0.7685 (mp10) REVERT: E 308 MET cc_start: 0.7866 (mmt) cc_final: 0.7512 (mmp) REVERT: E 342 GLN cc_start: 0.5508 (pt0) cc_final: 0.5116 (pp30) outliers start: 45 outliers final: 31 residues processed: 395 average time/residue: 0.1863 time to fit residues: 119.6605 Evaluate side-chains 375 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 338 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 595 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 761 SER Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 3 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 238 optimal weight: 0.7980 chunk 278 optimal weight: 10.0000 chunk 343 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS B 350 HIS D 605 ASN ** E 203 GLN ** 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 = 0.4143 r_free = 0.4143 target = 0.179310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137013 restraints weight = 56544.055| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.15 r_work: 0.3275 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31730 Z= 0.140 Angle : 0.713 17.541 42902 Z= 0.333 Chirality : 0.046 0.433 4810 Planarity : 0.004 0.059 5262 Dihedral : 14.160 151.944 6008 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.87 % Favored : 91.10 % Rotamer: Outliers : 1.34 % Allowed : 13.74 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.36 (0.14), residues: 3679 helix: 0.82 (0.14), residues: 1485 sheet: -2.51 (0.24), residues: 465 loop : -2.01 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 431 TYR 0.028 0.001 TYR E 74 PHE 0.037 0.001 PHE B 337 TRP 0.049 0.001 TRP E 138 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00331 (31658) covalent geometry : angle 0.68138 (42701) SS BOND : bond 0.00257 ( 15) SS BOND : angle 0.57925 ( 30) hydrogen bonds : bond 0.03167 ( 949) hydrogen bonds : angle 3.96986 ( 2762) link_ALPHA1-3 : bond 0.01649 ( 4) link_ALPHA1-3 : angle 2.43581 ( 12) link_ALPHA1-6 : bond 0.00616 ( 4) link_ALPHA1-6 : angle 1.40537 ( 12) link_BETA1-3 : bond 0.00461 ( 3) link_BETA1-3 : angle 5.06362 ( 9) link_BETA1-4 : bond 0.00832 ( 17) link_BETA1-4 : angle 2.26303 ( 51) link_NAG-ASN : bond 0.00845 ( 29) link_NAG-ASN : angle 3.98231 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 352 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7902 (mp10) REVERT: A 439 LEU cc_start: 0.7779 (pp) cc_final: 0.7495 (tt) REVERT: A 501 MET cc_start: 0.5872 (mtm) cc_final: 0.5461 (mtp) REVERT: A 664 MET cc_start: 0.6733 (mtp) cc_final: 0.6351 (mtm) REVERT: A 668 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6604 (pp) REVERT: A 770 MET cc_start: 0.7485 (tpt) cc_final: 0.6366 (tpt) REVERT: A 800 ARG cc_start: 0.7777 (tpt170) cc_final: 0.7414 (tpt90) REVERT: B 64 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8609 (mp) REVERT: B 292 ILE cc_start: 0.9044 (mm) cc_final: 0.8717 (mt) REVERT: B 540 ILE cc_start: 0.8414 (mm) cc_final: 0.7990 (mm) REVERT: C 54 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7947 (tp30) REVERT: C 200 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8054 (tttt) REVERT: C 315 PHE cc_start: 0.6923 (m-80) cc_final: 0.6640 (m-80) REVERT: C 531 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8248 (mmmm) REVERT: C 604 ASN cc_start: 0.8271 (t0) cc_final: 0.8038 (t0) REVERT: C 613 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.6828 (t60) REVERT: C 669 ASP cc_start: 0.7972 (t70) cc_final: 0.7674 (t0) REVERT: C 691 MET cc_start: 0.7819 (ttp) cc_final: 0.7480 (tmm) REVERT: C 705 MET cc_start: 0.8622 (mtp) cc_final: 0.8263 (mtt) REVERT: C 761 SER cc_start: 0.8839 (t) cc_final: 0.8581 (m) REVERT: C 770 MET cc_start: 0.8202 (tpt) cc_final: 0.7965 (tpt) REVERT: D 337 PHE cc_start: 0.8373 (t80) cc_final: 0.7825 (t80) REVERT: D 340 MET cc_start: 0.7431 (tpp) cc_final: 0.7065 (mpp) REVERT: D 800 ARG cc_start: 0.8447 (tpt170) cc_final: 0.8150 (tpt90) REVERT: E 62 TYR cc_start: 0.7544 (t80) cc_final: 0.7044 (t80) REVERT: E 101 ARG cc_start: 0.8677 (mtm110) cc_final: 0.8166 (mtm-85) REVERT: E 178 GLN cc_start: 0.8129 (mp10) cc_final: 0.7771 (mp10) REVERT: E 342 GLN cc_start: 0.5474 (pt0) cc_final: 0.5150 (pp30) outliers start: 42 outliers final: 28 residues processed: 383 average time/residue: 0.1795 time to fit residues: 112.2149 Evaluate side-chains 374 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 341 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 613 TRP Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 595 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 761 SER Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 249 optimal weight: 9.9990 chunk 178 optimal weight: 0.0570 chunk 185 optimal weight: 0.7980 chunk 183 optimal weight: 0.4980 chunk 265 optimal weight: 0.9980 chunk 151 optimal weight: 0.2980 chunk 267 optimal weight: 0.8980 chunk 286 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 234 optimal weight: 0.0030 chunk 113 optimal weight: 2.9990 overall best weight: 0.3308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.182116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143955 restraints weight = 54862.004| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.04 r_work: 0.3322 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31730 Z= 0.117 Angle : 0.697 17.185 42902 Z= 0.324 Chirality : 0.045 0.424 4810 Planarity : 0.004 0.060 5262 Dihedral : 13.710 148.699 6008 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.99 % Allowed : 14.39 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.15 (0.14), residues: 3679 helix: 1.04 (0.14), residues: 1488 sheet: -2.39 (0.24), residues: 463 loop : -1.95 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 431 TYR 0.025 0.001 TYR A 542 PHE 0.040 0.001 PHE B 337 TRP 0.050 0.001 TRP E 138 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00260 (31658) covalent geometry : angle 0.66563 (42701) SS BOND : bond 0.00282 ( 15) SS BOND : angle 0.57671 ( 30) hydrogen bonds : bond 0.02975 ( 949) hydrogen bonds : angle 3.88982 ( 2762) link_ALPHA1-3 : bond 0.01583 ( 4) link_ALPHA1-3 : angle 2.39837 ( 12) link_ALPHA1-6 : bond 0.00683 ( 4) link_ALPHA1-6 : angle 1.39368 ( 12) link_BETA1-3 : bond 0.00429 ( 3) link_BETA1-3 : angle 4.79600 ( 9) link_BETA1-4 : bond 0.00774 ( 17) link_BETA1-4 : angle 2.23992 ( 51) link_NAG-ASN : bond 0.00876 ( 29) link_NAG-ASN : angle 3.93976 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 362 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 LEU cc_start: 0.7699 (pp) cc_final: 0.7464 (tt) REVERT: A 485 ASP cc_start: 0.7392 (m-30) cc_final: 0.7191 (p0) REVERT: A 501 MET cc_start: 0.5886 (mtm) cc_final: 0.4929 (mtt) REVERT: A 664 MET cc_start: 0.6689 (mtp) cc_final: 0.6287 (mtm) REVERT: A 668 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6627 (pp) REVERT: A 770 MET cc_start: 0.7412 (tpt) cc_final: 0.6303 (tpt) REVERT: A 800 ARG cc_start: 0.7738 (tpt170) cc_final: 0.7395 (tpt90) REVERT: B 64 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 248 MET cc_start: 0.8245 (mmt) cc_final: 0.7915 (mmt) REVERT: B 292 ILE cc_start: 0.9019 (mm) cc_final: 0.8715 (mt) REVERT: B 800 ARG cc_start: 0.8020 (mmp80) cc_final: 0.7683 (mmp80) REVERT: C 54 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 200 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8003 (tttt) REVERT: C 482 LEU cc_start: 0.8445 (mt) cc_final: 0.7167 (mp) REVERT: C 531 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8449 (mmtp) REVERT: C 669 ASP cc_start: 0.7918 (t70) cc_final: 0.7641 (t0) REVERT: C 691 MET cc_start: 0.7729 (ttp) cc_final: 0.7393 (tmm) REVERT: C 705 MET cc_start: 0.8493 (mtp) cc_final: 0.8234 (mtt) REVERT: C 761 SER cc_start: 0.8895 (t) cc_final: 0.8622 (m) REVERT: C 770 MET cc_start: 0.8101 (tpt) cc_final: 0.7811 (tpt) REVERT: D 337 PHE cc_start: 0.8256 (t80) cc_final: 0.7701 (t80) REVERT: D 340 MET cc_start: 0.7383 (tpp) cc_final: 0.6934 (mpp) REVERT: D 584 PHE cc_start: 0.8285 (t80) cc_final: 0.7626 (m-10) REVERT: D 800 ARG cc_start: 0.8377 (tpt170) cc_final: 0.8108 (tpt90) REVERT: E 92 TYR cc_start: 0.8007 (t80) cc_final: 0.7763 (t80) REVERT: E 101 ARG cc_start: 0.8697 (mtm110) cc_final: 0.8175 (mtm-85) REVERT: E 178 GLN cc_start: 0.8022 (mp10) cc_final: 0.7670 (mp10) REVERT: E 211 ILE cc_start: 0.9233 (pt) cc_final: 0.8929 (mt) REVERT: E 308 MET cc_start: 0.7892 (mmt) cc_final: 0.7536 (mmp) outliers start: 31 outliers final: 22 residues processed: 386 average time/residue: 0.1772 time to fit residues: 112.1309 Evaluate side-chains 365 residues out of total 3209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 339 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 761 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 345 optimal weight: 8.9990 chunk 209 optimal weight: 0.6980 chunk 245 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 75 optimal weight: 0.1980 chunk 36 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.181066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142501 restraints weight = 63579.421| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.29 r_work: 0.3275 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31730 Z= 0.128 Angle : 0.703 17.039 42902 Z= 0.328 Chirality : 0.045 0.430 4810 Planarity : 0.004 0.060 5262 Dihedral : 13.531 145.445 6008 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.03 % Allowed : 14.64 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3679 helix: 1.06 (0.14), residues: 1493 sheet: -2.27 (0.24), residues: 471 loop : -1.93 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 431 TYR 0.024 0.001 TYR C 542 PHE 0.040 0.001 PHE B 337 TRP 0.052 0.001 TRP E 138 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00297 (31658) covalent geometry : angle 0.67215 (42701) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.97201 ( 30) hydrogen bonds : bond 0.03011 ( 949) hydrogen bonds : angle 3.88790 ( 2762) link_ALPHA1-3 : bond 0.01431 ( 4) link_ALPHA1-3 : angle 2.32276 ( 12) link_ALPHA1-6 : bond 0.00666 ( 4) link_ALPHA1-6 : angle 1.40299 ( 12) link_BETA1-3 : bond 0.00414 ( 3) link_BETA1-3 : angle 4.58601 ( 9) link_BETA1-4 : bond 0.00763 ( 17) link_BETA1-4 : angle 2.25130 ( 51) link_NAG-ASN : bond 0.00837 ( 29) link_NAG-ASN : angle 3.90133 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8785.83 seconds wall clock time: 151 minutes 2.67 seconds (9062.67 seconds total)