Starting phenix.real_space_refine on Fri Feb 6 23:40:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4n_48899/02_2026/9n4n_48899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4n_48899/02_2026/9n4n_48899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4n_48899/02_2026/9n4n_48899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4n_48899/02_2026/9n4n_48899.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4n_48899/02_2026/9n4n_48899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4n_48899/02_2026/9n4n_48899.cif" } resolution = 3.32 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= -0.073 sd= 1.231 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 16 5.49 5 S 164 5.16 5 C 18272 2.51 5 N 4534 2.21 5 O 5394 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 78 residue(s): 0.02s 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: 28384 Number of models: 1 Model: "" Number of chains: 18 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: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 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: {'PTRANS': 33, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "E" 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: "I" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "N" 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 295 Unusual residues: {'2J9': 1, 'NAG': 4, 'POV': 4} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} 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: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 309 Unusual residues: {'2J9': 1, 'NAG': 5, 'POV': 4} Classifications: {'peptide': 1, 'undetermined': 10} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 243 Unusual residues: {'2J9': 1, 'NAG': 4, 'POV': 3} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.88, per 1000 atoms: 0.35 Number of scatterers: 28384 At special positions: 0 Unit cell: (156.87, 117.03, 216.63, 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 164 16.00 P 16 15.00 F 4 9.00 O 5394 8.00 N 4534 7.00 C 18272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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 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 E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 5 " " BMA M 3 " - " MAN M 5 " BETA1-3 " BMA I 3 " - " BMA I 4 " " BMA N 3 " - " BMA N 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 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 B1005 " - " ASN B 67 " " NAG B1006 " - " ASN B 73 " " NAG B1007 " - " ASN B 412 " " NAG B1008 " - " ASN B 751 " " NAG C1006 " - " ASN C 67 " " NAG C1007 " - " ASN C 73 " " NAG C1008 " - " ASN C 275 " " NAG C1009 " - " ASN C 412 " " NAG C1010 " - " ASN C 751 " " NAG D1006 " - " ASN D 67 " " NAG D1007 " - " ASN D 73 " " NAG D1008 " - " ASN D 412 " " NAG D1009 " - " ASN D 751 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 546 " " NAG G 1 " - " ASN B 275 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN B 546 " " NAG J 1 " - " ASN C 378 " " NAG K 1 " - " ASN C 546 " " NAG L 1 " - " ASN D 275 " " NAG M 1 " - " ASN D 378 " " NAG N 1 " - " ASN D 546 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 2.1 seconds 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6304 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 36 sheets defined 42.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 removed outlier: 3.630A pdb=" N CYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.876A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.800A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (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 191 through 194 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.572A pdb=" N LYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.725A pdb=" N ALA A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.801A pdb=" N ARG A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.782A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.559A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.617A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.989A pdb=" N ARG A 458 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 459 " --> pdb=" O ASN A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 459' Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.716A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.664A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.740A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.740A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.532A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 655 removed outlier: 3.739A pdb=" N TRP A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.563A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.554A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.753A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.268A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.765A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 841 removed outlier: 3.569A pdb=" N VAL A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 854 removed outlier: 3.964A pdb=" N LYS A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.717A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.648A pdb=" N VAL B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 102 removed outlier: 3.736A pdb=" N GLN B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.909A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 removed outlier: 4.061A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.666A pdb=" N PHE B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.599A pdb=" N LEU B 182 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.859A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 245 removed outlier: 3.628A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.963A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 4.160A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.860A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.729A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.627A pdb=" N LEU B 505 " --> pdb=" O MET B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 567 through 584 removed outlier: 3.518A pdb=" N CYS B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 631 through 659 removed outlier: 3.916A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ALA B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 removed outlier: 3.551A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 710 removed outlier: 3.539A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.768A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.787A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.951A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.552A pdb=" N LYS B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 848 removed outlier: 3.852A pdb=" N ALA B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 841 " --> pdb=" O VAL B 837 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 867 removed outlier: 4.076A pdb=" N VAL B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU B 863 " --> pdb=" O SER B 859 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 867 " --> pdb=" O GLU B 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.630A pdb=" N CYS C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.876A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 4.799A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (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 191 through 194 Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.572A pdb=" N LYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 243 removed outlier: 3.725A pdb=" N ALA C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.801A pdb=" N ARG C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.782A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.558A pdb=" N LEU C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 removed outlier: 3.616A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.988A pdb=" N ARG C 458 " --> pdb=" O GLY C 455 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 459 " --> pdb=" O ASN C 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 459' Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.716A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.663A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.740A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.741A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.533A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 635 through 655 removed outlier: 3.739A pdb=" N TRP C 641 " --> pdb=" O GLY C 637 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.564A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.500A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.754A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 749 Processing helix chain 'C' and resid 773 through 788 removed outlier: 4.268A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 781 " --> pdb=" O LYS C 777 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.764A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 841 removed outlier: 3.569A pdb=" N VAL C 832 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 854 removed outlier: 3.965A pdb=" N LYS C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 852 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C 854 " --> pdb=" O ALA C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 3.718A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 863 " --> pdb=" O SER C 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.648A pdb=" N VAL D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 102 removed outlier: 3.736A pdb=" N GLN D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.909A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 161 removed outlier: 4.062A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.666A pdb=" N PHE D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.598A pdb=" N LEU D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.858A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 245 removed outlier: 3.628A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.963A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 4.161A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.859A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.729A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.627A pdb=" N LEU D 505 " --> pdb=" O MET D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 567 through 584 removed outlier: 3.518A pdb=" N CYS D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 631 through 659 removed outlier: 3.917A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ALA D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 658 " --> pdb=" O ASN D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 696 removed outlier: 3.551A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 710 removed outlier: 3.538A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP D 706 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 730 removed outlier: 3.769A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.788A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.951A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.551A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 848 removed outlier: 3.852A pdb=" N ALA D 828 " --> pdb=" O PHE D 824 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 841 " --> pdb=" O VAL D 837 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 842 " --> pdb=" O ALA D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 867 removed outlier: 4.076A pdb=" N VAL D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU D 863 " --> pdb=" O SER D 859 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 867 " --> pdb=" O GLU D 863 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 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: 3.620A 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 226 removed outlier: 6.357A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 370 removed outlier: 3.584A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 437 removed outlier: 6.482A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.527A pdb=" N PHE A 735 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 131 removed outlier: 8.273A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AB2, first strand: chain 'B' and resid 225 through 226 removed outlier: 6.612A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.726A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 389 through 390 Processing sheet with id=AB5, first strand: chain 'B' and resid 393 through 395 Processing sheet with id=AB6, first strand: chain 'B' and resid 434 through 436 removed outlier: 5.556A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.542A pdb=" N LYS B 762 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 681 through 683 removed outlier: 6.697A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 40 through 43 Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.620A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 225 through 226 removed outlier: 6.357A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE C 279 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 369 through 370 removed outlier: 3.584A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 432 through 437 removed outlier: 6.482A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 735 through 738 removed outlier: 3.526A pdb=" N PHE C 735 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain 'D' and resid 130 through 131 removed outlier: 8.273A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 175 through 176 Processing sheet with id=AD2, first strand: chain 'D' and resid 225 through 226 removed outlier: 6.612A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.726A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 389 through 390 Processing sheet with id=AD5, first strand: chain 'D' and resid 393 through 395 Processing sheet with id=AD6, first strand: chain 'D' and resid 434 through 436 removed outlier: 5.555A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD8, first strand: chain 'D' and resid 535 through 536 removed outlier: 3.542A pdb=" N LYS D 762 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 681 through 683 removed outlier: 6.697A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2429 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: 4.34 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4462 1.31 - 1.44: 7792 1.44 - 1.56: 16393 1.56 - 1.69: 57 1.69 - 1.82: 276 Bond restraints: 28980 Sorted by residual: bond pdb=" C ASN D 557 " pdb=" N PRO D 558 " ideal model delta sigma weight residual 1.337 1.399 -0.063 9.80e-03 1.04e+04 4.08e+01 bond pdb=" C ASN B 557 " pdb=" N PRO B 558 " ideal model delta sigma weight residual 1.337 1.399 -0.062 9.80e-03 1.04e+04 4.02e+01 bond pdb=" C1 NAG C1008 " pdb=" O5 NAG C1008 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C1 NAG A1008 " pdb=" O5 NAG A1008 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C1 NAG D1009 " pdb=" O5 NAG D1009 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.35e+01 ... (remaining 28975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 37131 2.99 - 5.97: 1602 5.97 - 8.96: 251 8.96 - 11.94: 87 11.94 - 14.93: 19 Bond angle restraints: 39090 Sorted by residual: angle pdb=" C SER D 856 " pdb=" N PHE D 857 " pdb=" CA PHE D 857 " ideal model delta sigma weight residual 120.82 130.48 -9.66 1.50e+00 4.44e-01 4.15e+01 angle pdb=" C SER B 856 " pdb=" N PHE B 857 " pdb=" CA PHE B 857 " ideal model delta sigma weight residual 120.82 130.43 -9.61 1.50e+00 4.44e-01 4.11e+01 angle pdb=" C SER D 429 " pdb=" N ASN D 430 " pdb=" CA ASN D 430 " ideal model delta sigma weight residual 120.79 128.86 -8.07 1.39e+00 5.18e-01 3.37e+01 angle pdb=" C SER B 429 " pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 120.79 128.75 -7.96 1.39e+00 5.18e-01 3.28e+01 angle pdb=" CA GLU D 808 " pdb=" CB GLU D 808 " pdb=" CG GLU D 808 " ideal model delta sigma weight residual 114.10 124.91 -10.81 2.00e+00 2.50e-01 2.92e+01 ... (remaining 39085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 17415 33.82 - 67.64: 633 67.64 - 101.47: 173 101.47 - 135.29: 81 135.29 - 169.11: 4 Dihedral angle restraints: 18306 sinusoidal: 8510 harmonic: 9796 Sorted by residual: dihedral pdb=" CA GLU D 441 " pdb=" C GLU D 441 " pdb=" N PRO D 442 " pdb=" CA PRO D 442 " ideal model delta harmonic sigma weight residual -180.00 -101.43 -78.57 0 5.00e+00 4.00e-02 2.47e+02 dihedral pdb=" CA GLU B 441 " pdb=" C GLU B 441 " pdb=" N PRO B 442 " pdb=" CA PRO B 442 " ideal model delta harmonic sigma weight residual -180.00 -101.46 -78.54 0 5.00e+00 4.00e-02 2.47e+02 dihedral pdb=" CA SER B 809 " pdb=" C SER B 809 " pdb=" N LYS B 810 " pdb=" CA LYS B 810 " ideal model delta harmonic sigma weight residual 180.00 117.49 62.51 0 5.00e+00 4.00e-02 1.56e+02 ... (remaining 18303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4282 0.144 - 0.289: 114 0.289 - 0.433: 16 0.433 - 0.577: 4 0.577 - 0.722: 2 Chirality restraints: 4418 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 378 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 378 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG D1007 " pdb=" ND2 ASN D 73 " pdb=" C2 NAG D1007 " pdb=" O5 NAG D1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.94e+00 ... (remaining 4415 not shown) Planarity restraints: 4834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 108 " 0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO D 109 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 109 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 109 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 108 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO B 109 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 109 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 109 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 853 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C GLU C 853 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU C 853 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS C 854 " 0.021 2.00e-02 2.50e+03 ... (remaining 4831 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7373 2.80 - 3.32: 24300 3.32 - 3.85: 44451 3.85 - 4.37: 53611 4.37 - 4.90: 91435 Nonbonded interactions: 221170 Sorted by model distance: nonbonded pdb=" OG SER B 393 " pdb=" O7 NAG G 1 " model vdw 2.273 3.040 nonbonded pdb=" OG SER D 393 " pdb=" O7 NAG L 1 " model vdw 2.274 3.040 nonbonded pdb=" O LYS D 629 " pdb=" OG1 THR D 633 " model vdw 2.286 3.040 nonbonded pdb=" O LYS B 629 " pdb=" OG1 THR B 633 " model vdw 2.286 3.040 nonbonded pdb=" OG SER C 670 " pdb=" OD1 ASP C 672 " model vdw 2.286 3.040 ... (remaining 221165 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 874 or resid 1003 thro \ ugh 1004 or resid 1006 through 1008)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 874 or resid 1003 thro \ ugh 1004 or resid 1006 through 1008)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 874 or resid 1003 thro \ ugh 1004 or resid 1006 through 1008)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 874 or resid 1003 thro \ ugh 1004 or resid 1006 through 1008)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'N' } 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: 3.370 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 28.300 Find NCS groups from input model: 0.800 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: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.010 0.120 29042 Z= 0.465 Angle : 1.520 14.978 39268 Z= 0.792 Chirality : 0.067 0.722 4418 Planarity : 0.008 0.096 4806 Dihedral : 20.174 169.110 11978 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.95 % Favored : 86.52 % Rotamer: Outliers : 0.48 % Allowed : 5.04 % Favored : 94.48 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.62 % 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: -6.20 (0.10), residues: 3364 helix: -4.59 (0.06), residues: 1414 sheet: -3.62 (0.22), residues: 404 loop : -3.68 (0.13), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 184 TYR 0.034 0.003 TYR C 733 PHE 0.046 0.003 PHE B 735 TRP 0.040 0.004 TRP B 134 HIS 0.016 0.003 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00986 (28980) covalent geometry : angle 1.49615 (39090) SS BOND : bond 0.00229 ( 8) SS BOND : angle 1.40880 ( 16) hydrogen bonds : bond 0.30513 ( 841) hydrogen bonds : angle 10.75113 ( 2429) link_ALPHA1-3 : bond 0.00974 ( 4) link_ALPHA1-3 : angle 3.54941 ( 12) link_ALPHA1-6 : bond 0.00215 ( 4) link_ALPHA1-6 : angle 1.61851 ( 12) link_BETA1-3 : bond 0.01111 ( 2) link_BETA1-3 : angle 4.14245 ( 6) link_BETA1-4 : bond 0.01440 ( 16) link_BETA1-4 : angle 3.97866 ( 48) link_NAG-ASN : bond 0.01363 ( 28) link_NAG-ASN : angle 5.04203 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 608 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6913 (mp) REVERT: A 699 ILE cc_start: 0.8312 (tp) cc_final: 0.8071 (mt) REVERT: A 780 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7861 (mp) REVERT: B 323 MET cc_start: 0.8441 (tpp) cc_final: 0.8102 (tpt) REVERT: B 608 LEU cc_start: 0.8237 (tm) cc_final: 0.7563 (tp) REVERT: B 776 ASP cc_start: 0.8309 (m-30) cc_final: 0.8070 (m-30) REVERT: B 780 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8444 (mp) REVERT: C 487 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7749 (mtpp) REVERT: C 524 GLU cc_start: 0.6818 (tp30) cc_final: 0.6592 (mm-30) REVERT: C 632 SER cc_start: 0.6911 (m) cc_final: 0.6490 (p) REVERT: C 664 MET cc_start: 0.5515 (mpt) cc_final: 0.5263 (ttt) REVERT: C 780 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7458 (mp) REVERT: C 793 MET cc_start: 0.7662 (mtt) cc_final: 0.7395 (mtp) REVERT: D 323 MET cc_start: 0.8657 (tpp) cc_final: 0.8441 (tpt) REVERT: D 351 LYS cc_start: 0.7574 (ttmp) cc_final: 0.7341 (tptt) REVERT: D 542 TYR cc_start: 0.7836 (t80) cc_final: 0.7569 (t80) REVERT: D 565 MET cc_start: 0.7543 (ttm) cc_final: 0.7330 (mmt) REVERT: D 608 LEU cc_start: 0.8079 (tm) cc_final: 0.7406 (tp) REVERT: D 669 ASP cc_start: 0.7552 (t70) cc_final: 0.7172 (p0) REVERT: D 776 ASP cc_start: 0.8384 (m-30) cc_final: 0.8136 (m-30) REVERT: D 780 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8325 (mp) outliers start: 8 outliers final: 0 residues processed: 616 average time/residue: 0.1954 time to fit residues: 186.1939 Evaluate side-chains 357 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 352 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 136 HIS A 141 ASN A 348 ASN A 367 HIS A 495 ASN A 596 ASN A 604 ASN A 747 GLN B 84 ASN B 98 GLN B 123 ASN B 141 ASN B 241 GLN B 591 ASN B 604 ASN B 654 ASN B 802 ASN B 819 ASN B 872 GLN C 98 GLN C 129 HIS C 136 HIS C 141 ASN C 348 ASN C 495 ASN C 596 ASN C 604 ASN C 622 GLN C 747 GLN C 802 ASN D 84 ASN D 98 GLN D 141 ASN D 241 GLN D 283 ASN D 348 ASN D 591 ASN D 604 ASN D 621 GLN D 654 ASN D 802 ASN D 819 ASN D 872 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.213000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192194 restraints weight = 49029.041| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.00 r_work: 0.3846 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29042 Z= 0.160 Angle : 0.866 15.886 39268 Z= 0.414 Chirality : 0.051 0.641 4418 Planarity : 0.006 0.073 4806 Dihedral : 21.240 159.212 5572 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.07 % Favored : 88.66 % Rotamer: Outliers : 1.77 % Allowed : 9.13 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.37 % 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: -4.73 (0.12), residues: 3364 helix: -2.88 (0.10), residues: 1414 sheet: -3.35 (0.22), residues: 430 loop : -3.24 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 220 TYR 0.034 0.002 TYR C 590 PHE 0.034 0.002 PHE B 735 TRP 0.024 0.002 TRP B 798 HIS 0.008 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00349 (28980) covalent geometry : angle 0.83791 (39090) SS BOND : bond 0.00508 ( 8) SS BOND : angle 1.11805 ( 16) hydrogen bonds : bond 0.04465 ( 841) hydrogen bonds : angle 5.44481 ( 2429) link_ALPHA1-3 : bond 0.01498 ( 4) link_ALPHA1-3 : angle 3.62356 ( 12) link_ALPHA1-6 : bond 0.01315 ( 4) link_ALPHA1-6 : angle 3.05466 ( 12) link_BETA1-3 : bond 0.01069 ( 2) link_BETA1-3 : angle 4.57949 ( 6) link_BETA1-4 : bond 0.01033 ( 16) link_BETA1-4 : angle 2.99951 ( 48) link_NAG-ASN : bond 0.00733 ( 28) link_NAG-ASN : angle 3.69242 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 388 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7087 (mp) REVERT: A 645 LEU cc_start: 0.8738 (tp) cc_final: 0.8410 (tp) REVERT: A 652 THR cc_start: 0.8797 (t) cc_final: 0.8585 (m) REVERT: A 732 ASP cc_start: 0.7653 (t70) cc_final: 0.7391 (p0) REVERT: B 323 MET cc_start: 0.8762 (tpp) cc_final: 0.8322 (tpt) REVERT: B 367 HIS cc_start: 0.6475 (t-90) cc_final: 0.6222 (t-90) REVERT: B 738 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 776 ASP cc_start: 0.8349 (m-30) cc_final: 0.7977 (m-30) REVERT: B 780 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8688 (mp) REVERT: C 524 GLU cc_start: 0.6543 (tp30) cc_final: 0.5581 (tp30) REVERT: C 632 SER cc_start: 0.7519 (m) cc_final: 0.7023 (p) REVERT: D 583 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.7388 (tpp-160) REVERT: D 691 MET cc_start: 0.8236 (ttp) cc_final: 0.7899 (tmm) REVERT: D 703 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7144 (m-30) REVERT: D 738 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7575 (mm-30) REVERT: D 776 ASP cc_start: 0.8370 (m-30) cc_final: 0.8070 (m-30) REVERT: D 780 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8647 (mp) REVERT: D 800 ARG cc_start: 0.7181 (tpp-160) cc_final: 0.6895 (tpp-160) outliers start: 46 outliers final: 20 residues processed: 421 average time/residue: 0.1830 time to fit residues: 123.0434 Evaluate side-chains 356 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 703 ASP Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 117 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 287 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 327 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.209165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.187603 restraints weight = 51494.390| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.18 r_work: 0.3781 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29042 Z= 0.168 Angle : 0.813 13.570 39268 Z= 0.383 Chirality : 0.050 0.536 4418 Planarity : 0.005 0.072 4806 Dihedral : 18.590 145.915 5568 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.11 % Favored : 87.68 % Rotamer: Outliers : 1.87 % Allowed : 10.87 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.13), residues: 3364 helix: -1.62 (0.12), residues: 1400 sheet: -3.05 (0.23), residues: 420 loop : -3.00 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 220 TYR 0.026 0.002 TYR C 590 PHE 0.023 0.002 PHE A 166 TRP 0.026 0.002 TRP D 498 HIS 0.006 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00384 (28980) covalent geometry : angle 0.78543 (39090) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.26046 ( 16) hydrogen bonds : bond 0.04092 ( 841) hydrogen bonds : angle 4.95184 ( 2429) link_ALPHA1-3 : bond 0.02061 ( 4) link_ALPHA1-3 : angle 2.48135 ( 12) link_ALPHA1-6 : bond 0.01708 ( 4) link_ALPHA1-6 : angle 2.18545 ( 12) link_BETA1-3 : bond 0.01019 ( 2) link_BETA1-3 : angle 3.59522 ( 6) link_BETA1-4 : bond 0.00855 ( 16) link_BETA1-4 : angle 3.09756 ( 48) link_NAG-ASN : bond 0.00985 ( 28) link_NAG-ASN : angle 3.72819 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 340 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7234 (mp) REVERT: A 652 THR cc_start: 0.8780 (t) cc_final: 0.8558 (m) REVERT: A 732 ASP cc_start: 0.7642 (t70) cc_final: 0.7301 (p0) REVERT: B 323 MET cc_start: 0.8775 (tpp) cc_final: 0.8253 (tpt) REVERT: B 738 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 776 ASP cc_start: 0.8405 (m-30) cc_final: 0.8068 (m-30) REVERT: B 780 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8616 (mp) REVERT: C 313 ASP cc_start: 0.7077 (t0) cc_final: 0.6866 (t0) REVERT: C 524 GLU cc_start: 0.6668 (tp30) cc_final: 0.6320 (mm-30) REVERT: C 632 SER cc_start: 0.7527 (m) cc_final: 0.7097 (p) REVERT: C 854 LYS cc_start: 0.4986 (OUTLIER) cc_final: 0.4446 (tmmt) REVERT: D 677 GLN cc_start: 0.7472 (pp30) cc_final: 0.7197 (pt0) REVERT: D 798 TRP cc_start: 0.8224 (m100) cc_final: 0.7916 (m100) REVERT: D 800 ARG cc_start: 0.7311 (tpp-160) cc_final: 0.7015 (tpp-160) outliers start: 49 outliers final: 29 residues processed: 375 average time/residue: 0.1798 time to fit residues: 109.8086 Evaluate side-chains 337 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 296 optimal weight: 0.7980 chunk 250 optimal weight: 20.0000 chunk 258 optimal weight: 0.6980 chunk 240 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 320 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN B 98 GLN C 610 ASN C 654 ASN D 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.209218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.182222 restraints weight = 36712.782| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.83 r_work: 0.3705 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29042 Z= 0.149 Angle : 0.780 19.759 39268 Z= 0.365 Chirality : 0.049 0.503 4418 Planarity : 0.005 0.076 4806 Dihedral : 17.465 140.840 5566 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.96 % Favored : 87.86 % Rotamer: Outliers : 2.18 % Allowed : 11.65 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.14), residues: 3364 helix: -0.88 (0.14), residues: 1400 sheet: -2.85 (0.24), residues: 414 loop : -2.86 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.022 0.002 TYR A 86 PHE 0.030 0.002 PHE D 228 TRP 0.018 0.002 TRP B 798 HIS 0.004 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00339 (28980) covalent geometry : angle 0.74711 (39090) SS BOND : bond 0.00207 ( 8) SS BOND : angle 1.26402 ( 16) hydrogen bonds : bond 0.03494 ( 841) hydrogen bonds : angle 4.68729 ( 2429) link_ALPHA1-3 : bond 0.01665 ( 4) link_ALPHA1-3 : angle 2.74785 ( 12) link_ALPHA1-6 : bond 0.01281 ( 4) link_ALPHA1-6 : angle 2.55931 ( 12) link_BETA1-3 : bond 0.01011 ( 2) link_BETA1-3 : angle 3.88149 ( 6) link_BETA1-4 : bond 0.00748 ( 16) link_BETA1-4 : angle 2.80610 ( 48) link_NAG-ASN : bond 0.01106 ( 28) link_NAG-ASN : angle 4.11419 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 320 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7412 (mm) REVERT: A 652 THR cc_start: 0.8839 (t) cc_final: 0.8629 (m) REVERT: A 664 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.5094 (mpt) REVERT: A 732 ASP cc_start: 0.7748 (t70) cc_final: 0.7314 (p0) REVERT: A 780 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 315 PHE cc_start: 0.6779 (m-10) cc_final: 0.6270 (m-80) REVERT: B 776 ASP cc_start: 0.8346 (m-30) cc_final: 0.8071 (m-30) REVERT: B 780 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 798 TRP cc_start: 0.8133 (m100) cc_final: 0.7821 (m100) REVERT: C 218 MET cc_start: 0.8240 (ttm) cc_final: 0.7934 (ttm) REVERT: C 524 GLU cc_start: 0.6655 (tp30) cc_final: 0.6113 (tp30) REVERT: C 664 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5241 (mpt) REVERT: C 780 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 854 LYS cc_start: 0.5351 (OUTLIER) cc_final: 0.4560 (tmmt) REVERT: D 800 ARG cc_start: 0.7514 (tpp-160) cc_final: 0.7157 (tpp-160) outliers start: 58 outliers final: 29 residues processed: 362 average time/residue: 0.1703 time to fit residues: 100.1252 Evaluate side-chains 333 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 129 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 335 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 13 optimal weight: 0.0470 chunk 232 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS B 456 ASN C 367 HIS D 98 GLN D 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.209671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.186733 restraints weight = 51006.640| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.25 r_work: 0.3762 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29042 Z= 0.139 Angle : 0.761 15.622 39268 Z= 0.354 Chirality : 0.048 0.475 4418 Planarity : 0.005 0.077 4806 Dihedral : 16.609 140.965 5564 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.85 % Favored : 87.98 % Rotamer: Outliers : 2.08 % Allowed : 11.99 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -2.63 (0.14), residues: 3364 helix: -0.44 (0.14), residues: 1418 sheet: -2.68 (0.25), residues: 376 loop : -2.77 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.024 0.001 TYR A 86 PHE 0.021 0.001 PHE A 166 TRP 0.017 0.002 TRP B 296 HIS 0.004 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00315 (28980) covalent geometry : angle 0.72937 (39090) SS BOND : bond 0.00328 ( 8) SS BOND : angle 1.15130 ( 16) hydrogen bonds : bond 0.03348 ( 841) hydrogen bonds : angle 4.52482 ( 2429) link_ALPHA1-3 : bond 0.01618 ( 4) link_ALPHA1-3 : angle 2.39409 ( 12) link_ALPHA1-6 : bond 0.01265 ( 4) link_ALPHA1-6 : angle 2.38532 ( 12) link_BETA1-3 : bond 0.01063 ( 2) link_BETA1-3 : angle 3.95849 ( 6) link_BETA1-4 : bond 0.00662 ( 16) link_BETA1-4 : angle 2.73198 ( 48) link_NAG-ASN : bond 0.01020 ( 28) link_NAG-ASN : angle 3.97152 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7267 (mm) REVERT: A 635 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7181 (mp) REVERT: A 652 THR cc_start: 0.8845 (t) cc_final: 0.8603 (m) REVERT: A 664 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5291 (mpt) REVERT: A 732 ASP cc_start: 0.7583 (t70) cc_final: 0.7251 (p0) REVERT: A 770 MET cc_start: 0.8346 (tpt) cc_final: 0.8041 (tpt) REVERT: B 776 ASP cc_start: 0.8408 (m-30) cc_final: 0.8130 (m-30) REVERT: B 780 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8602 (mp) REVERT: C 218 MET cc_start: 0.8245 (ttm) cc_final: 0.8017 (ttm) REVERT: C 524 GLU cc_start: 0.6645 (tp30) cc_final: 0.6094 (tp30) REVERT: C 664 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.5375 (mpt) REVERT: C 780 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 854 LYS cc_start: 0.5056 (OUTLIER) cc_final: 0.4582 (tmmt) REVERT: D 583 ARG cc_start: 0.7930 (mmp-170) cc_final: 0.7435 (tpp-160) REVERT: D 798 TRP cc_start: 0.8268 (m100) cc_final: 0.7928 (m100) REVERT: D 800 ARG cc_start: 0.7440 (tpp-160) cc_final: 0.6716 (tpp-160) outliers start: 55 outliers final: 30 residues processed: 363 average time/residue: 0.1720 time to fit residues: 100.5909 Evaluate side-chains 338 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 301 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 281 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 266 optimal weight: 0.5980 chunk 140 optimal weight: 20.0000 chunk 129 optimal weight: 0.0070 chunk 72 optimal weight: 5.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN C 34 HIS C 367 HIS C 591 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.217081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181397 restraints weight = 62921.539| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.96 r_work: 0.3849 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29042 Z= 0.128 Angle : 0.738 15.858 39268 Z= 0.344 Chirality : 0.047 0.463 4418 Planarity : 0.004 0.078 4806 Dihedral : 15.747 141.077 5564 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.25 % Favored : 88.60 % Rotamer: Outliers : 1.77 % Allowed : 12.77 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -2.32 (0.14), residues: 3364 helix: -0.13 (0.14), residues: 1424 sheet: -2.62 (0.26), residues: 356 loop : -2.66 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 800 TYR 0.023 0.001 TYR A 86 PHE 0.020 0.001 PHE B 228 TRP 0.019 0.001 TRP B 798 HIS 0.004 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00284 (28980) covalent geometry : angle 0.70610 (39090) SS BOND : bond 0.00417 ( 8) SS BOND : angle 1.18236 ( 16) hydrogen bonds : bond 0.03176 ( 841) hydrogen bonds : angle 4.45681 ( 2429) link_ALPHA1-3 : bond 0.01475 ( 4) link_ALPHA1-3 : angle 2.18617 ( 12) link_ALPHA1-6 : bond 0.01314 ( 4) link_ALPHA1-6 : angle 2.28643 ( 12) link_BETA1-3 : bond 0.01104 ( 2) link_BETA1-3 : angle 4.11718 ( 6) link_BETA1-4 : bond 0.00606 ( 16) link_BETA1-4 : angle 2.66213 ( 48) link_NAG-ASN : bond 0.00927 ( 28) link_NAG-ASN : angle 3.92528 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 327 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7359 (mm) REVERT: A 413 MET cc_start: 0.8180 (mtt) cc_final: 0.7978 (mtt) REVERT: A 635 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7038 (mp) REVERT: A 652 THR cc_start: 0.8935 (t) cc_final: 0.8718 (m) REVERT: A 664 MET cc_start: 0.5385 (OUTLIER) cc_final: 0.4893 (mpt) REVERT: A 703 ASP cc_start: 0.7256 (m-30) cc_final: 0.6914 (m-30) REVERT: A 793 MET cc_start: 0.7751 (mtt) cc_final: 0.7510 (mtp) REVERT: B 36 LEU cc_start: 0.8409 (tt) cc_final: 0.8166 (tp) REVERT: B 323 MET cc_start: 0.8717 (tpt) cc_final: 0.8305 (tpt) REVERT: B 776 ASP cc_start: 0.8296 (m-30) cc_final: 0.8086 (m-30) REVERT: C 218 MET cc_start: 0.8408 (ttm) cc_final: 0.8197 (ttm) REVERT: C 524 GLU cc_start: 0.6731 (tp30) cc_final: 0.6299 (tp30) REVERT: C 625 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7461 (mt-10) REVERT: C 664 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.5056 (mpt) REVERT: C 726 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7386 (mm-40) REVERT: C 770 MET cc_start: 0.8301 (tpt) cc_final: 0.7894 (tpt) REVERT: D 565 MET cc_start: 0.8325 (ttp) cc_final: 0.8107 (ttp) REVERT: D 608 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7109 (tp) REVERT: D 798 TRP cc_start: 0.8304 (m100) cc_final: 0.7867 (m100) REVERT: D 800 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.7046 (ttp80) outliers start: 48 outliers final: 27 residues processed: 365 average time/residue: 0.1811 time to fit residues: 106.3520 Evaluate side-chains 339 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 307 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 329 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN B 754 GLN C 84 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 654 ASN D 98 GLN D 754 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.203899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.180539 restraints weight = 47729.409| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.15 r_work: 0.3698 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29042 Z= 0.225 Angle : 0.816 15.356 39268 Z= 0.386 Chirality : 0.051 0.440 4418 Planarity : 0.005 0.091 4806 Dihedral : 15.501 140.180 5562 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.45 % Favored : 86.31 % Rotamer: Outliers : 1.98 % Allowed : 12.91 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -2.46 (0.14), residues: 3364 helix: -0.27 (0.14), residues: 1408 sheet: -2.46 (0.27), residues: 370 loop : -2.76 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 800 TYR 0.029 0.002 TYR C 590 PHE 0.022 0.002 PHE C 533 TRP 0.021 0.002 TRP C 589 HIS 0.008 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00552 (28980) covalent geometry : angle 0.78699 (39090) SS BOND : bond 0.00167 ( 8) SS BOND : angle 1.01926 ( 16) hydrogen bonds : bond 0.03698 ( 841) hydrogen bonds : angle 4.64887 ( 2429) link_ALPHA1-3 : bond 0.01352 ( 4) link_ALPHA1-3 : angle 2.52009 ( 12) link_ALPHA1-6 : bond 0.01022 ( 4) link_ALPHA1-6 : angle 2.12419 ( 12) link_BETA1-3 : bond 0.01084 ( 2) link_BETA1-3 : angle 4.17069 ( 6) link_BETA1-4 : bond 0.00507 ( 16) link_BETA1-4 : angle 2.77280 ( 48) link_NAG-ASN : bond 0.00872 ( 28) link_NAG-ASN : angle 3.91716 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7365 (mm) REVERT: A 218 MET cc_start: 0.8265 (ttm) cc_final: 0.7921 (ttm) REVERT: A 635 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7283 (mp) REVERT: A 664 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.5177 (mpt) REVERT: A 703 ASP cc_start: 0.7064 (m-30) cc_final: 0.6838 (m-30) REVERT: A 770 MET cc_start: 0.8351 (tpt) cc_final: 0.8144 (tpt) REVERT: B 323 MET cc_start: 0.8758 (tpt) cc_final: 0.8378 (tpt) REVERT: C 524 GLU cc_start: 0.6676 (tp30) cc_final: 0.6319 (tp30) REVERT: C 664 MET cc_start: 0.5551 (OUTLIER) cc_final: 0.5169 (mpt) REVERT: C 770 MET cc_start: 0.8363 (tpt) cc_final: 0.8109 (tpt) REVERT: D 323 MET cc_start: 0.8861 (tpp) cc_final: 0.8376 (tpt) REVERT: D 565 MET cc_start: 0.8459 (ttp) cc_final: 0.8238 (ttp) REVERT: D 583 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.7636 (tpp-160) outliers start: 54 outliers final: 37 residues processed: 354 average time/residue: 0.1779 time to fit residues: 101.7201 Evaluate side-chains 329 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 243 optimal weight: 0.2980 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 591 ASN D 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.205296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179635 restraints weight = 37276.855| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.69 r_work: 0.3694 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29042 Z= 0.182 Angle : 0.777 15.334 39268 Z= 0.367 Chirality : 0.049 0.428 4418 Planarity : 0.005 0.088 4806 Dihedral : 15.019 140.400 5562 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.05 % Favored : 87.77 % Rotamer: Outliers : 1.94 % Allowed : 13.62 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -2.39 (0.14), residues: 3364 helix: -0.18 (0.14), residues: 1404 sheet: -2.46 (0.27), residues: 386 loop : -2.71 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 800 TYR 0.026 0.002 TYR A 86 PHE 0.019 0.002 PHE A 476 TRP 0.020 0.002 TRP B 296 HIS 0.006 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00437 (28980) covalent geometry : angle 0.74906 (39090) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.96527 ( 16) hydrogen bonds : bond 0.03465 ( 841) hydrogen bonds : angle 4.57758 ( 2429) link_ALPHA1-3 : bond 0.01361 ( 4) link_ALPHA1-3 : angle 2.32427 ( 12) link_ALPHA1-6 : bond 0.01041 ( 4) link_ALPHA1-6 : angle 1.64911 ( 12) link_BETA1-3 : bond 0.01043 ( 2) link_BETA1-3 : angle 4.36711 ( 6) link_BETA1-4 : bond 0.00488 ( 16) link_BETA1-4 : angle 2.64915 ( 48) link_NAG-ASN : bond 0.00893 ( 28) link_NAG-ASN : angle 3.74927 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7392 (mm) REVERT: A 218 MET cc_start: 0.8347 (ttm) cc_final: 0.8015 (ttm) REVERT: A 635 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7156 (mp) REVERT: A 664 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4873 (mpt) REVERT: A 703 ASP cc_start: 0.7072 (m-30) cc_final: 0.6802 (m-30) REVERT: A 732 ASP cc_start: 0.7655 (t70) cc_final: 0.7398 (p0) REVERT: B 323 MET cc_start: 0.8750 (tpt) cc_final: 0.8398 (tpt) REVERT: B 583 ARG cc_start: 0.7950 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: C 524 GLU cc_start: 0.6651 (tp30) cc_final: 0.6295 (tp30) REVERT: C 664 MET cc_start: 0.5369 (OUTLIER) cc_final: 0.4826 (mpt) REVERT: C 747 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: C 770 MET cc_start: 0.8248 (tpt) cc_final: 0.8031 (tpt) REVERT: D 583 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7460 (tpp-160) REVERT: D 780 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8663 (mp) outliers start: 53 outliers final: 35 residues processed: 343 average time/residue: 0.1669 time to fit residues: 92.3968 Evaluate side-chains 339 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 101 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 210 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 255 optimal weight: 0.1980 chunk 199 optimal weight: 4.9990 chunk 167 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.206725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.188549 restraints weight = 54947.360| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.93 r_work: 0.3786 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29042 Z= 0.143 Angle : 0.760 15.366 39268 Z= 0.357 Chirality : 0.048 0.424 4418 Planarity : 0.005 0.090 4806 Dihedral : 14.820 140.598 5562 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.17 % Favored : 87.65 % Rotamer: Outliers : 1.70 % Allowed : 14.24 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.19 % 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: -2.28 (0.15), residues: 3364 helix: -0.08 (0.14), residues: 1404 sheet: -2.42 (0.27), residues: 386 loop : -2.67 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 800 TYR 0.026 0.001 TYR A 86 PHE 0.020 0.002 PHE D 228 TRP 0.017 0.001 TRP B 798 HIS 0.005 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00331 (28980) covalent geometry : angle 0.73252 (39090) SS BOND : bond 0.00157 ( 8) SS BOND : angle 0.93402 ( 16) hydrogen bonds : bond 0.03334 ( 841) hydrogen bonds : angle 4.52574 ( 2429) link_ALPHA1-3 : bond 0.01389 ( 4) link_ALPHA1-3 : angle 2.21252 ( 12) link_ALPHA1-6 : bond 0.01031 ( 4) link_ALPHA1-6 : angle 1.61037 ( 12) link_BETA1-3 : bond 0.01081 ( 2) link_BETA1-3 : angle 4.35685 ( 6) link_BETA1-4 : bond 0.00520 ( 16) link_BETA1-4 : angle 2.59039 ( 48) link_NAG-ASN : bond 0.00902 ( 28) link_NAG-ASN : angle 3.71125 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7212 (mm) REVERT: A 218 MET cc_start: 0.8278 (ttm) cc_final: 0.7967 (ttm) REVERT: A 635 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7167 (mp) REVERT: A 664 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.5073 (mpt) REVERT: A 732 ASP cc_start: 0.7538 (t70) cc_final: 0.7262 (p0) REVERT: A 747 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6124 (mp10) REVERT: B 323 MET cc_start: 0.8676 (tpt) cc_final: 0.8382 (tpt) REVERT: B 583 ARG cc_start: 0.7875 (tpp-160) cc_final: 0.7374 (tpp-160) REVERT: C 524 GLU cc_start: 0.6583 (tp30) cc_final: 0.6233 (tp30) REVERT: C 664 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.5000 (mpt) REVERT: C 747 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: D 583 ARG cc_start: 0.8150 (tpp-160) cc_final: 0.7408 (tpp-160) REVERT: D 780 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 46 outliers final: 33 residues processed: 338 average time/residue: 0.1906 time to fit residues: 103.8874 Evaluate side-chains 338 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 187 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 241 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 223 optimal weight: 0.7980 chunk 111 optimal weight: 0.0070 chunk 313 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 328 HIS ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.217194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.180522 restraints weight = 51606.409| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.55 r_work: 0.3889 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29042 Z= 0.119 Angle : 0.725 15.273 39268 Z= 0.341 Chirality : 0.047 0.414 4418 Planarity : 0.005 0.088 4806 Dihedral : 13.960 141.456 5562 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.92 % Favored : 89.02 % Rotamer: Outliers : 1.36 % Allowed : 14.61 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.19 % 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: -1.99 (0.15), residues: 3364 helix: 0.17 (0.15), residues: 1418 sheet: -2.36 (0.28), residues: 356 loop : -2.51 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 220 TYR 0.024 0.001 TYR A 86 PHE 0.021 0.001 PHE D 228 TRP 0.016 0.001 TRP D 498 HIS 0.004 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00258 (28980) covalent geometry : angle 0.69762 (39090) SS BOND : bond 0.00289 ( 8) SS BOND : angle 0.70813 ( 16) hydrogen bonds : bond 0.03066 ( 841) hydrogen bonds : angle 4.37486 ( 2429) link_ALPHA1-3 : bond 0.01340 ( 4) link_ALPHA1-3 : angle 1.92358 ( 12) link_ALPHA1-6 : bond 0.00897 ( 4) link_ALPHA1-6 : angle 1.28300 ( 12) link_BETA1-3 : bond 0.01103 ( 2) link_BETA1-3 : angle 4.48556 ( 6) link_BETA1-4 : bond 0.00514 ( 16) link_BETA1-4 : angle 2.36243 ( 48) link_NAG-ASN : bond 0.00888 ( 28) link_NAG-ASN : angle 3.66529 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 321 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8408 (ttm) cc_final: 0.8064 (ttm) REVERT: A 635 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7009 (mp) REVERT: A 664 MET cc_start: 0.5239 (OUTLIER) cc_final: 0.4688 (mpt) REVERT: A 747 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6147 (mp10) REVERT: A 793 MET cc_start: 0.7617 (mtt) cc_final: 0.7353 (mtp) REVERT: B 298 MET cc_start: 0.7442 (mtm) cc_final: 0.7233 (mtt) REVERT: B 323 MET cc_start: 0.8681 (tpt) cc_final: 0.8326 (tpt) REVERT: B 337 PHE cc_start: 0.8481 (t80) cc_final: 0.8155 (t80) REVERT: B 583 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.7310 (tpp-160) REVERT: B 755 ILE cc_start: 0.8384 (mm) cc_final: 0.8099 (mt) REVERT: B 788 GLU cc_start: 0.7849 (mp0) cc_final: 0.7626 (mt-10) REVERT: C 524 GLU cc_start: 0.6645 (tp30) cc_final: 0.6289 (tp30) REVERT: C 664 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4681 (mpt) REVERT: C 679 LYS cc_start: 0.7104 (tptt) cc_final: 0.6798 (pttt) REVERT: C 726 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7492 (mm-40) REVERT: C 747 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: D 36 LEU cc_start: 0.8254 (tt) cc_final: 0.7720 (tp) REVERT: D 583 ARG cc_start: 0.8207 (tpp-160) cc_final: 0.7376 (tpp-160) REVERT: D 608 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7032 (tp) REVERT: D 780 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8574 (mp) REVERT: D 798 TRP cc_start: 0.8238 (m100) cc_final: 0.7876 (m100) outliers start: 36 outliers final: 23 residues processed: 347 average time/residue: 0.1830 time to fit residues: 101.8460 Evaluate side-chains 330 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 213 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 231 optimal weight: 0.5980 chunk 97 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 104 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 98 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.217474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.182749 restraints weight = 58551.084| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.68 r_work: 0.3865 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29042 Z= 0.124 Angle : 0.720 15.194 39268 Z= 0.339 Chirality : 0.047 0.400 4418 Planarity : 0.005 0.090 4806 Dihedral : 13.492 141.088 5562 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.46 % Favored : 88.48 % Rotamer: Outliers : 1.33 % Allowed : 14.48 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.15 % 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: -1.85 (0.15), residues: 3364 helix: 0.29 (0.15), residues: 1418 sheet: -2.28 (0.28), residues: 356 loop : -2.46 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 220 TYR 0.024 0.001 TYR A 86 PHE 0.020 0.001 PHE D 228 TRP 0.028 0.001 TRP D 706 HIS 0.004 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00276 (28980) covalent geometry : angle 0.69340 (39090) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.71162 ( 16) hydrogen bonds : bond 0.03058 ( 841) hydrogen bonds : angle 4.34719 ( 2429) link_ALPHA1-3 : bond 0.01276 ( 4) link_ALPHA1-3 : angle 1.89444 ( 12) link_ALPHA1-6 : bond 0.00837 ( 4) link_ALPHA1-6 : angle 1.28705 ( 12) link_BETA1-3 : bond 0.01095 ( 2) link_BETA1-3 : angle 4.61381 ( 6) link_BETA1-4 : bond 0.00518 ( 16) link_BETA1-4 : angle 2.32367 ( 48) link_NAG-ASN : bond 0.00879 ( 28) link_NAG-ASN : angle 3.63474 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6266.88 seconds wall clock time: 108 minutes 21.53 seconds (6501.53 seconds total)