Starting phenix.real_space_refine on Thu May 22 14:37:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmp_38485/05_2025/8xmp_38485_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmp_38485/05_2025/8xmp_38485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmp_38485/05_2025/8xmp_38485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmp_38485/05_2025/8xmp_38485.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmp_38485/05_2025/8xmp_38485_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmp_38485/05_2025/8xmp_38485_neut.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.040 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 Ca 23 9.91 5 Fe 2 7.16 5 S 218 5.16 5 C 14198 2.51 5 N 4085 2.21 5 O 4423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22949 Number of models: 1 Model: "" Number of chains: 15 Chain: "2" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "E" Number of atoms: 5455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5455 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 22, 'TRANS': 695} Chain breaks: 5 Chain: "F" Number of atoms: 6370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6370 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 24, 'TRANS': 816} Chain breaks: 3 Chain: "D" Number of atoms: 6369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6369 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 24, 'TRANS': 816} Chain breaks: 3 Chain: "C" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" 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: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 33 Unusual residues: {' CA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 51 Unusual residues: {' CA': 9, 'NAG': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 51 Unusual residues: {' CA': 9, 'NAG': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.69, per 1000 atoms: 0.55 Number of scatterers: 22949 At special positions: 0 Unit cell: (138.03, 135.89, 173.34, 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) Fe 2 26.01 Ca 23 19.99 S 218 16.00 O 4423 8.00 N 4085 7.00 C 14198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=93, symmetry=0 Simple disulfide: pdb=" SG CYS 2 52 " - pdb=" SG CYS 2 86 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 90 " - pdb=" SG CYS 2 207 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 250 " - pdb=" SG CYS 2 281 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 292 " - pdb=" SG CYS 2 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 355 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 365 " distance=2.03 Simple disulfide: pdb=" SG CYS E 335 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 462 " distance=2.03 Simple disulfide: pdb=" SG CYS E 411 " - pdb=" SG CYS E 472 " distance=2.03 Simple disulfide: pdb=" SG CYS E 442 " - pdb=" SG CYS E 452 " distance=2.03 Simple disulfide: pdb=" SG CYS E 487 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 567 " distance=2.03 Simple disulfide: pdb=" SG CYS E 516 " - pdb=" SG CYS E 577 " distance=2.03 Simple disulfide: pdb=" SG CYS E 547 " - pdb=" SG CYS E 557 " distance=2.03 Simple disulfide: pdb=" SG CYS E 592 " - pdb=" SG CYS E 626 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 621 " - pdb=" SG CYS E 682 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 662 " distance=2.03 Simple disulfide: pdb=" SG CYS E 728 " - pdb=" SG CYS E 762 " distance=2.03 Simple disulfide: pdb=" SG CYS E 744 " - pdb=" SG CYS E 808 " distance=2.03 Simple disulfide: pdb=" SG CYS E 757 " - pdb=" SG CYS E 818 " distance=2.03 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 798 " distance=2.03 Simple disulfide: pdb=" SG CYS E 835 " - pdb=" SG CYS E 869 " distance=2.03 Simple disulfide: pdb=" SG CYS E 864 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E 895 " - pdb=" SG CYS E 905 " distance=2.03 Simple disulfide: pdb=" SG CYS E 938 " - pdb=" SG CYS E 972 " distance=2.03 Simple disulfide: pdb=" SG CYS E 954 " - pdb=" SG CYS E1018 " distance=2.03 Simple disulfide: pdb=" SG CYS E 967 " - pdb=" SG CYS E1028 " distance=2.03 Simple disulfide: pdb=" SG CYS E 998 " - pdb=" SG CYS E1008 " distance=2.03 Simple disulfide: pdb=" SG CYS F 168 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 258 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 238 " distance=2.03 Simple disulfide: pdb=" SG CYS F 275 " - pdb=" SG CYS F 309 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 355 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 365 " distance=2.03 Simple disulfide: pdb=" SG CYS F 335 " - pdb=" SG CYS F 345 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 416 " distance=2.02 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 472 " distance=2.03 Simple disulfide: pdb=" SG CYS F 442 " - pdb=" SG CYS F 452 " distance=2.03 Simple disulfide: pdb=" SG CYS F 487 " - pdb=" SG CYS F 521 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 567 " distance=2.03 Simple disulfide: pdb=" SG CYS F 516 " - pdb=" SG CYS F 577 " distance=2.03 Simple disulfide: pdb=" SG CYS F 547 " - pdb=" SG CYS F 557 " distance=2.03 Simple disulfide: pdb=" SG CYS F 592 " - pdb=" SG CYS F 626 " distance=2.03 Simple disulfide: pdb=" SG CYS F 608 " - pdb=" SG CYS F 672 " distance=2.03 Simple disulfide: pdb=" SG CYS F 621 " - pdb=" SG CYS F 682 " distance=2.03 Simple disulfide: pdb=" SG CYS F 652 " - pdb=" SG CYS F 662 " distance=2.03 Simple disulfide: pdb=" SG CYS F 728 " - pdb=" SG CYS F 762 " distance=2.03 Simple disulfide: pdb=" SG CYS F 744 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 757 " - pdb=" SG CYS F 818 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 798 " distance=2.03 Simple disulfide: pdb=" SG CYS F 835 " - pdb=" SG CYS F 869 " distance=2.03 Simple disulfide: pdb=" SG CYS F 864 " - pdb=" SG CYS F 925 " distance=2.03 Simple disulfide: pdb=" SG CYS F 895 " - pdb=" SG CYS F 905 " distance=2.03 Simple disulfide: pdb=" SG CYS F 938 " - pdb=" SG CYS F 972 " distance=2.03 Simple disulfide: pdb=" SG CYS F 954 " - pdb=" SG CYS F1018 " distance=2.03 Simple disulfide: pdb=" SG CYS F 967 " - pdb=" SG CYS F1028 " distance=2.03 Simple disulfide: pdb=" SG CYS F 998 " - pdb=" SG CYS F1008 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.01 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.03 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS D 592 " - pdb=" SG CYS D 626 " distance=2.03 Simple disulfide: pdb=" SG CYS D 608 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 682 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 662 " distance=2.03 Simple disulfide: pdb=" SG CYS D 728 " - pdb=" SG CYS D 762 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 808 " distance=2.02 Simple disulfide: pdb=" SG CYS D 757 " - pdb=" SG CYS D 818 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 835 " - pdb=" SG CYS D 869 " distance=2.03 Simple disulfide: pdb=" SG CYS D 864 " - pdb=" SG CYS D 925 " distance=2.03 Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.03 Simple disulfide: pdb=" SG CYS D 938 " - pdb=" SG CYS D 972 " distance=2.03 Simple disulfide: pdb=" SG CYS D 954 " - pdb=" SG CYS D1018 " distance=2.03 Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " 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=2, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG 2 401 " - " ASN 2 125 " " NAG 2 402 " - " ASN 2 182 " " NAG A 1 " - " ASN 2 148 " " NAG D1101 " - " ASN D 445 " " NAG D1102 " - " ASN D 767 " " NAG D1103 " - " ASN D1027 " " NAG E1101 " - " ASN E 767 " " NAG E1102 " - " ASN E1027 " " NAG F1101 " - " ASN F 445 " " NAG F1102 " - " ASN F 767 " " NAG F1103 " - " ASN F1027 " " NAG X 1 " - " ASN F 320 " " NAG Y 1 " - " ASN D 320 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.7 seconds 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5268 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 55 sheets defined 24.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain '2' and resid 141 through 146 Processing helix chain '2' and resid 157 through 162 removed outlier: 4.009A pdb=" N THR 2 161 " --> pdb=" O ASP 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 255 Processing helix chain '2' and resid 333 through 346 removed outlier: 4.517A pdb=" N ASP 2 338 " --> pdb=" O THR 2 334 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP 2 339 " --> pdb=" O SER 2 335 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU 2 346 " --> pdb=" O LYS 2 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.542A pdb=" N GLU E 359 " --> pdb=" O ASN E 356 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 360 " --> pdb=" O HIS E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 360' Processing helix chain 'E' and resid 403 through 415 Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 474 through 476 No H-bonds generated for 'chain 'E' and resid 474 through 476' Processing helix chain 'E' and resid 503 through 507 removed outlier: 4.057A pdb=" N PHE E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 613 through 624 Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'E' and resid 794 through 798 Processing helix chain 'E' and resid 809 through 813 removed outlier: 3.675A pdb=" N GLU E 812 " --> pdb=" O ARG E 809 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 813 " --> pdb=" O HIS E 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 809 through 813' Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 901 through 905 Processing helix chain 'E' and resid 959 through 971 Processing helix chain 'E' and resid 1004 through 1008 Processing helix chain 'E' and resid 1019 through 1023 removed outlier: 3.732A pdb=" N ASP E1023 " --> pdb=" O HIS E1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.805A pdb=" N ASP F 253 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 341 through 345 removed outlier: 3.717A pdb=" N GLN F 344 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS F 345 " --> pdb=" O ILE F 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 341 through 345' Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 403 through 415 removed outlier: 3.557A pdb=" N VAL F 409 " --> pdb=" O LYS F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.863A pdb=" N PHE F 507 " --> pdb=" O ASP F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 568 through 572 removed outlier: 3.539A pdb=" N ASP F 572 " --> pdb=" O HIS F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 624 Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.691A pdb=" N ASP F 813 " --> pdb=" O HIS F 810 " (cutoff:3.500A) Processing helix chain 'F' and resid 856 through 867 Processing helix chain 'F' and resid 901 through 905 removed outlier: 3.715A pdb=" N GLN F 904 " --> pdb=" O THR F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 920 removed outlier: 3.560A pdb=" N GLU F 920 " --> pdb=" O PRO F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 959 through 971 removed outlier: 3.511A pdb=" N ALA F 963 " --> pdb=" O ASP F 959 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1023 removed outlier: 3.565A pdb=" N GLU F1022 " --> pdb=" O GLY F1019 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP F1023 " --> pdb=" O HIS F1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1019 through 1023' Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.542A pdb=" N CYS D 238 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.508A pdb=" N ASP D 360 " --> pdb=" O HIS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 504 through 507 removed outlier: 4.057A pdb=" N PHE D 507 " --> pdb=" O ASP D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 613 through 624 removed outlier: 3.586A pdb=" N ALA D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 removed outlier: 3.707A pdb=" N VAL D 755 " --> pdb=" O SER D 751 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 756 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 760 " --> pdb=" O VAL D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 798 removed outlier: 3.592A pdb=" N CYS D 798 " --> pdb=" O ILE D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 813 Processing helix chain 'D' and resid 856 through 868 Processing helix chain 'D' and resid 901 through 905 removed outlier: 3.778A pdb=" N GLN D 904 " --> pdb=" O THR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 971 Processing helix chain 'D' and resid 1019 through 1023 removed outlier: 3.599A pdb=" N ASP D1023 " --> pdb=" O HIS D1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.609A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.693A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'G' and resid 4 through 17 removed outlier: 4.014A pdb=" N LYS G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 4.217A pdb=" N GLY G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 46 removed outlier: 3.813A pdb=" N GLU G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER G 44 " --> pdb=" O PHE G 41 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY G 46 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 57 through 77 Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.834A pdb=" N THR G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR G 87 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 119 removed outlier: 3.954A pdb=" N PHE G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG G 104 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 123 through 141 Processing sheet with id=AA1, first strand: chain '2' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain '2' and resid 170 through 172 removed outlier: 4.158A pdb=" N LEU 2 164 " --> pdb=" O VAL 2 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 238 through 243 removed outlier: 7.705A pdb=" N VAL 2 219 " --> pdb=" O HIS 2 303 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS 2 303 " --> pdb=" O VAL 2 219 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER 2 223 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA 2 299 " --> pdb=" O SER 2 223 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY 2 314 " --> pdb=" O PHE 2 300 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL 2 302 " --> pdb=" O ALA 2 312 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA 2 312 " --> pdb=" O VAL 2 302 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP 2 304 " --> pdb=" O TRP 2 310 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TRP 2 310 " --> pdb=" O ASP 2 304 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL 2 329 " --> pdb=" O SER 2 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 266 through 273 removed outlier: 4.084A pdb=" N GLY E 271 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 276 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 364 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 266 through 273 removed outlier: 4.084A pdb=" N GLY E 271 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 276 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS E 327 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 371 through 377 removed outlier: 7.027A pdb=" N THR E 471 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 396 through 397 removed outlier: 6.958A pdb=" N LYS E 396 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU E 439 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 477 through 481 removed outlier: 4.033A pdb=" N THR E 498 " --> pdb=" O HIS E 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 477 through 481 Processing sheet with id=AB1, first strand: chain 'E' and resid 544 through 545 Processing sheet with id=AB2, first strand: chain 'E' and resid 583 through 586 Processing sheet with id=AB3, first strand: chain 'E' and resid 583 through 586 removed outlier: 6.918A pdb=" N ILE E 681 " --> pdb=" O LEU E 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 649 through 650 Processing sheet with id=AB5, first strand: chain 'E' and resid 719 through 722 Processing sheet with id=AB6, first strand: chain 'E' and resid 719 through 722 removed outlier: 6.047A pdb=" N GLY E 815 " --> pdb=" O ALA E 768 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA E 768 " --> pdb=" O GLY E 815 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE E 817 " --> pdb=" O ILE E 766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 823 through 827 removed outlier: 3.935A pdb=" N TRP E 922 " --> pdb=" O ASN E 876 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 874 " --> pdb=" O THR E 924 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 823 through 827 removed outlier: 6.437A pdb=" N LEU E 839 " --> pdb=" O VAL E 850 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP E 889 " --> pdb=" O TRP E 847 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR E 849 " --> pdb=" O TRP E 889 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 930 through 932 removed outlier: 6.849A pdb=" N ASN E1027 " --> pdb=" O LEU E 976 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 930 through 932 removed outlier: 5.975A pdb=" N VAL E 942 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 953 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TRP E 992 " --> pdb=" O TRP E 950 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR E 952 " --> pdb=" O TRP E 992 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AC3, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.723A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.723A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 279 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 290 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N TRP F 287 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N LEU F 330 " --> pdb=" O TRP F 287 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 289 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 371 through 377 removed outlier: 6.858A pdb=" N THR F 471 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 371 through 377 removed outlier: 6.000A pdb=" N VAL F 386 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU F 437 " --> pdb=" O LEU F 394 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS F 396 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU F 439 " --> pdb=" O LYS F 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 477 through 481 Processing sheet with id=AC9, first strand: chain 'F' and resid 477 through 481 removed outlier: 6.324A pdb=" N VAL F 491 " --> pdb=" O ILE F 502 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 502 " --> pdb=" O VAL F 491 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 498 " --> pdb=" O HIS F 495 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TRP F 541 " --> pdb=" O TRP F 499 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER F 501 " --> pdb=" O TRP F 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 543 through 545 Processing sheet with id=AD2, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.826A pdb=" N ILE F 681 " --> pdb=" O LEU F 630 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.207A pdb=" N VAL F 596 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 607 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TRP F 646 " --> pdb=" O TRP F 604 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER F 606 " --> pdb=" O TRP F 646 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 649 through 650 Processing sheet with id=AD5, first strand: chain 'F' and resid 719 through 722 removed outlier: 6.012A pdb=" N GLY F 815 " --> pdb=" O ALA F 768 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA F 768 " --> pdb=" O GLY F 815 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 817 " --> pdb=" O ILE F 766 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 719 through 722 removed outlier: 14.862A pdb=" N GLY F 730 " --> pdb=" O ASP F 745 " (cutoff:3.500A) removed outlier: 11.135A pdb=" N ASP F 745 " --> pdb=" O GLY F 730 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL F 732 " --> pdb=" O ILE F 743 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 743 " --> pdb=" O VAL F 732 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 781 " --> pdb=" O TRP F 740 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR F 742 " --> pdb=" O ILE F 781 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU F 783 " --> pdb=" O THR F 742 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU F 785 " --> pdb=" O CYS F 744 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP F 746 " --> pdb=" O GLU F 785 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 823 through 827 removed outlier: 3.694A pdb=" N TRP F 922 " --> pdb=" O ASN F 876 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 823 through 827 removed outlier: 6.566A pdb=" N LEU F 839 " --> pdb=" O VAL F 850 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 850 " --> pdb=" O LEU F 839 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP F 889 " --> pdb=" O TRP F 847 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR F 849 " --> pdb=" O TRP F 889 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 929 through 932 removed outlier: 6.204A pdb=" N VAL F 942 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 953 " --> pdb=" O VAL F 942 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N TRP F 950 " --> pdb=" O ILE F 991 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N LEU F 993 " --> pdb=" O TRP F 950 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR F 952 " --> pdb=" O LEU F 993 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 929 through 932 Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AE3, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AE4, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.696A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.696A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS D 327 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 371 through 380 removed outlier: 5.927A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR D 471 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 371 through 380 removed outlier: 5.927A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU D 439 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 440 " --> pdb=" O ASN D 454 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN D 454 " --> pdb=" O SER D 440 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 476 through 481 Processing sheet with id=AE9, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.398A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 500 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TRP D 499 " --> pdb=" O GLN D 539 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 543 through 545 Processing sheet with id=AF2, first strand: chain 'D' and resid 583 through 586 removed outlier: 7.228A pdb=" N ILE D 681 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 583 through 586 removed outlier: 5.280A pdb=" N VAL D 596 " --> pdb=" O LEU D 607 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TRP D 646 " --> pdb=" O TRP D 604 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER D 606 " --> pdb=" O TRP D 646 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AF5, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=AF6, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=AF7, first strand: chain 'D' and resid 823 through 827 removed outlier: 4.158A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 874 " --> pdb=" O THR D 924 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 823 through 827 removed outlier: 6.227A pdb=" N LEU D 839 " --> pdb=" O VAL D 850 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP D 889 " --> pdb=" O TRP D 847 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR D 849 " --> pdb=" O TRP D 889 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 929 through 932 removed outlier: 6.220A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TRP D 992 " --> pdb=" O TRP D 950 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR D 952 " --> pdb=" O TRP D 992 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 929 through 932 872 hydrogen bonds defined for protein. 2352 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: 10.98 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 9284 1.38 - 1.55: 13928 1.55 - 1.72: 1 1.72 - 1.89: 247 1.89 - 2.06: 8 Bond restraints: 23468 Sorted by residual: bond pdb=" CA SER D 473 " pdb=" CB SER D 473 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.30e-02 5.92e+03 1.63e+01 bond pdb=" CA SER E 473 " pdb=" CB SER E 473 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.57e-02 4.06e+03 7.57e+00 bond pdb=" N ASP D 745 " pdb=" CA ASP D 745 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" N THR E 471 " pdb=" CA THR E 471 " ideal model delta sigma weight residual 1.464 1.493 -0.030 1.25e-02 6.40e+03 5.64e+00 bond pdb=" CA ALA E 474 " pdb=" CB ALA E 474 " ideal model delta sigma weight residual 1.530 1.492 0.039 1.69e-02 3.50e+03 5.21e+00 ... (remaining 23463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 31437 1.98 - 3.95: 359 3.95 - 5.93: 29 5.93 - 7.90: 1 7.90 - 9.88: 2 Bond angle restraints: 31828 Sorted by residual: angle pdb=" N HIS D 475 " pdb=" CA HIS D 475 " pdb=" C HIS D 475 " ideal model delta sigma weight residual 110.97 101.63 9.34 1.09e+00 8.42e-01 7.34e+01 angle pdb=" N ALA D 474 " pdb=" CA ALA D 474 " pdb=" C ALA D 474 " ideal model delta sigma weight residual 113.50 103.62 9.88 1.65e+00 3.67e-01 3.58e+01 angle pdb=" C HIS D 475 " pdb=" CA HIS D 475 " pdb=" CB HIS D 475 " ideal model delta sigma weight residual 110.96 116.89 -5.93 1.54e+00 4.22e-01 1.48e+01 angle pdb=" CA SER E 473 " pdb=" C SER E 473 " pdb=" O SER E 473 " ideal model delta sigma weight residual 120.90 117.29 3.61 1.03e+00 9.43e-01 1.23e+01 angle pdb=" CA CYS E 472 " pdb=" C CYS E 472 " pdb=" O CYS E 472 " ideal model delta sigma weight residual 121.88 118.12 3.76 1.13e+00 7.83e-01 1.11e+01 ... (remaining 31823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12659 17.88 - 35.76: 1127 35.76 - 53.65: 216 53.65 - 71.53: 45 71.53 - 89.41: 22 Dihedral angle restraints: 14069 sinusoidal: 5804 harmonic: 8265 Sorted by residual: dihedral pdb=" CB CYS F 275 " pdb=" SG CYS F 275 " pdb=" SG CYS F 309 " pdb=" CB CYS F 309 " ideal model delta sinusoidal sigma weight residual 93.00 169.36 -76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS E 291 " pdb=" SG CYS E 291 " pdb=" SG CYS E 355 " pdb=" CB CYS E 355 " ideal model delta sinusoidal sigma weight residual 93.00 158.99 -65.99 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS D 275 " pdb=" SG CYS D 275 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual -86.00 -138.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 14066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2694 0.050 - 0.099: 595 0.099 - 0.149: 114 0.149 - 0.198: 3 0.198 - 0.248: 1 Chirality restraints: 3407 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" CA PHE F 283 " pdb=" N PHE F 283 " pdb=" C PHE F 283 " pdb=" CB PHE F 283 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO F 591 " pdb=" N PRO F 591 " pdb=" C PRO F 591 " pdb=" CB PRO F 591 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 3404 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 903 " 0.013 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP D 903 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 903 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 903 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 903 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 903 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 903 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 903 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 903 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 903 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 903 " 0.012 2.00e-02 2.50e+03 1.73e-02 7.50e+00 pdb=" CG TRP F 903 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP F 903 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP F 903 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 903 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP F 903 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 903 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 903 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 903 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 903 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 281 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C VAL F 281 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL F 281 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG F 282 " 0.013 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 313 2.60 - 3.18: 19227 3.18 - 3.75: 37612 3.75 - 4.33: 52720 4.33 - 4.90: 86501 Nonbonded interactions: 196373 Sorted by model distance: nonbonded pdb=" OE2 GLU D 812 " pdb="CA CA D1107 " model vdw 2.025 2.510 nonbonded pdb=" OH TYR 2 254 " pdb=" O TYR 2 327 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP E 784 " pdb="CA CA E1105 " model vdw 2.163 2.510 nonbonded pdb=" O MET F 786 " pdb="CA CA F1107 " model vdw 2.168 2.510 nonbonded pdb=" OD1 ASP F 749 " pdb="CA CA F1107 " model vdw 2.182 2.510 ... (remaining 196368 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' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = (chain 'D' and (resid 154 through 828 or resid 835 through 1030 or resid 1101 th \ rough 1112)) selection = (chain 'F' and (resid 154 through 691 or resid 718 through 1030 or resid 1101 th \ rough 1112)) } 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 52.990 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 23579 Z= 0.151 Angle : 0.527 9.879 32062 Z= 0.296 Chirality : 0.042 0.248 3407 Planarity : 0.003 0.053 4125 Dihedral : 13.857 89.408 8522 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 0.12 % Allowed : 0.16 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2934 helix: 1.68 (0.23), residues: 532 sheet: -0.83 (0.26), residues: 401 loop : -0.82 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 903 HIS 0.007 0.001 HIS C 122 PHE 0.009 0.001 PHE 2 280 TYR 0.013 0.001 TYR 2 221 ARG 0.003 0.000 ARG F 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 13) link_NAG-ASN : angle 1.15704 ( 39) link_BETA1-4 : bond 0.00352 ( 3) link_BETA1-4 : angle 1.25924 ( 9) hydrogen bonds : bond 0.21931 ( 765) hydrogen bonds : angle 8.32673 ( 2352) SS BOND : bond 0.00324 ( 93) SS BOND : angle 0.93970 ( 186) covalent geometry : bond 0.00308 (23468) covalent geometry : angle 0.52185 (31828) Misc. bond : bond 0.09347 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 494 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 156 LYS cc_start: 0.8160 (tttt) cc_final: 0.7829 (tttp) REVERT: 2 184 SER cc_start: 0.8877 (m) cc_final: 0.8516 (p) REVERT: 2 202 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.6935 (mmm160) REVERT: 2 248 ASP cc_start: 0.8031 (m-30) cc_final: 0.7799 (m-30) REVERT: 2 306 GLU cc_start: 0.7361 (mp0) cc_final: 0.6976 (mp0) REVERT: 2 308 ASP cc_start: 0.8519 (t0) cc_final: 0.8150 (t0) REVERT: 2 341 GLN cc_start: 0.7587 (mm110) cc_final: 0.7326 (mt0) REVERT: E 299 ASP cc_start: 0.6206 (m-30) cc_final: 0.5978 (m-30) REVERT: E 442 CYS cc_start: 0.4242 (t) cc_final: 0.3760 (t) REVERT: E 532 HIS cc_start: 0.8508 (t-90) cc_final: 0.8251 (t70) REVERT: E 544 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7240 (tt0) REVERT: E 550 HIS cc_start: 0.7559 (p90) cc_final: 0.7238 (p90) REVERT: E 615 GLU cc_start: 0.7551 (mp0) cc_final: 0.7275 (mp0) REVERT: E 764 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7636 (pt0) REVERT: E 938 CYS cc_start: 0.6522 (m) cc_final: 0.6165 (m) REVERT: E 995 GLU cc_start: 0.7228 (tt0) cc_final: 0.6739 (tm-30) REVERT: E 997 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6230 (mmtt) REVERT: E 999 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7387 (mmtt) REVERT: F 167 MET cc_start: 0.5833 (mmp) cc_final: 0.5542 (ttp) REVERT: F 187 ASN cc_start: 0.8639 (t0) cc_final: 0.7812 (t0) REVERT: F 240 HIS cc_start: 0.6341 (p90) cc_final: 0.5484 (p90) REVERT: F 253 ASP cc_start: 0.7111 (m-30) cc_final: 0.6879 (m-30) REVERT: F 446 GLU cc_start: 0.7728 (mp0) cc_final: 0.7335 (mp0) REVERT: F 612 TRP cc_start: 0.7678 (t-100) cc_final: 0.7413 (t-100) REVERT: F 649 MET cc_start: 0.8157 (mtm) cc_final: 0.7827 (mtt) REVERT: F 723 ASN cc_start: 0.7812 (t0) cc_final: 0.7577 (m-40) REVERT: F 859 THR cc_start: 0.7949 (m) cc_final: 0.7691 (p) REVERT: F 922 TRP cc_start: 0.8159 (m100) cc_final: 0.7941 (m100) REVERT: F 1011 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7620 (ttp-170) REVERT: D 177 GLN cc_start: 0.7286 (mp10) cc_final: 0.7034 (mt0) REVERT: D 245 LYS cc_start: 0.8015 (mptt) cc_final: 0.7815 (tttp) REVERT: D 456 GLN cc_start: 0.8897 (mt0) cc_final: 0.8696 (mt0) REVERT: D 550 HIS cc_start: 0.7838 (p-80) cc_final: 0.7583 (p-80) REVERT: D 825 ARG cc_start: 0.8365 (ptt180) cc_final: 0.8015 (ptt-90) REVERT: D 1004 SER cc_start: 0.8528 (p) cc_final: 0.8267 (t) REVERT: G 9 SER cc_start: 0.8764 (p) cc_final: 0.8486 (p) REVERT: G 132 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8667 (mtpp) outliers start: 3 outliers final: 1 residues processed: 496 average time/residue: 0.3698 time to fit residues: 275.6377 Evaluate side-chains 250 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 473 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 6.9990 chunk 223 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 231 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN E 475 HIS E 539 GLN E 550 HIS E 723 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 946 HIS ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 GLN F 306 GLN F 464 HIS F 587 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 HIS D 964 GLN D 986 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145175 restraints weight = 28955.812| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.17 r_work: 0.3376 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 23579 Z= 0.167 Angle : 0.572 9.905 32062 Z= 0.301 Chirality : 0.045 0.258 3407 Planarity : 0.004 0.049 4125 Dihedral : 5.950 78.581 3476 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 1.44 % Allowed : 8.59 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2934 helix: 1.88 (0.23), residues: 532 sheet: -0.93 (0.25), residues: 410 loop : -0.86 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 922 HIS 0.008 0.001 HIS F 495 PHE 0.014 0.001 PHE 2 300 TYR 0.018 0.001 TYR 2 183 ARG 0.007 0.001 ARG F 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 13) link_NAG-ASN : angle 1.99586 ( 39) link_BETA1-4 : bond 0.00133 ( 3) link_BETA1-4 : angle 1.19204 ( 9) hydrogen bonds : bond 0.04450 ( 765) hydrogen bonds : angle 5.62325 ( 2352) SS BOND : bond 0.00403 ( 93) SS BOND : angle 1.20097 ( 186) covalent geometry : bond 0.00397 (23468) covalent geometry : angle 0.56221 (31828) Misc. bond : bond 0.10400 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.7923 (mmm160) REVERT: 2 308 ASP cc_start: 0.8644 (t0) cc_final: 0.8351 (t0) REVERT: 2 337 GLN cc_start: 0.8403 (tt0) cc_final: 0.8064 (mt0) REVERT: 2 341 GLN cc_start: 0.8282 (mm110) cc_final: 0.8074 (mt0) REVERT: E 299 ASP cc_start: 0.6145 (m-30) cc_final: 0.5782 (m-30) REVERT: E 327 HIS cc_start: 0.7216 (m-70) cc_final: 0.7006 (m90) REVERT: E 406 GLU cc_start: 0.7543 (mp0) cc_final: 0.7308 (mp0) REVERT: E 532 HIS cc_start: 0.8619 (t-90) cc_final: 0.8383 (t70) REVERT: E 544 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7035 (tt0) REVERT: E 615 GLU cc_start: 0.7888 (mp0) cc_final: 0.7544 (mp0) REVERT: E 745 ASP cc_start: 0.8820 (p0) cc_final: 0.8439 (p0) REVERT: E 764 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7801 (pt0) REVERT: E 891 ASP cc_start: 0.8573 (t0) cc_final: 0.8330 (t0) REVERT: E 938 CYS cc_start: 0.6900 (m) cc_final: 0.6559 (m) REVERT: E 970 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7469 (mp) REVERT: E 995 GLU cc_start: 0.7376 (tt0) cc_final: 0.6733 (tm-30) REVERT: E 997 LYS cc_start: 0.6917 (mmtt) cc_final: 0.6184 (mmtt) REVERT: F 167 MET cc_start: 0.6273 (mmp) cc_final: 0.5728 (ttp) REVERT: F 187 ASN cc_start: 0.8810 (t0) cc_final: 0.8163 (t0) REVERT: F 240 HIS cc_start: 0.6545 (p90) cc_final: 0.5843 (p90) REVERT: F 346 LYS cc_start: 0.7554 (mmtm) cc_final: 0.7104 (ptmm) REVERT: F 352 LYS cc_start: 0.7595 (tttm) cc_final: 0.7064 (tmtt) REVERT: F 446 GLU cc_start: 0.7996 (mp0) cc_final: 0.7738 (mp0) REVERT: F 541 TRP cc_start: 0.8682 (m100) cc_final: 0.8385 (m100) REVERT: F 649 MET cc_start: 0.8414 (mtm) cc_final: 0.8179 (mtt) REVERT: F 723 ASN cc_start: 0.8134 (t0) cc_final: 0.7894 (m-40) REVERT: F 914 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7892 (mp) REVERT: F 922 TRP cc_start: 0.8331 (m100) cc_final: 0.7843 (m100) REVERT: D 622 GLN cc_start: 0.8622 (tp40) cc_final: 0.8385 (tp40) REVERT: D 740 TRP cc_start: 0.8301 (m100) cc_final: 0.8070 (m100) REVERT: D 825 ARG cc_start: 0.8728 (ptt180) cc_final: 0.8225 (ptt-90) REVERT: D 922 TRP cc_start: 0.8378 (m100) cc_final: 0.8102 (m100) outliers start: 35 outliers final: 20 residues processed: 298 average time/residue: 0.3404 time to fit residues: 157.9433 Evaluate side-chains 250 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 970 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 964 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 30 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 203 optimal weight: 0.0970 chunk 216 optimal weight: 0.0000 chunk 4 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN E 456 GLN E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS D 986 GLN G 2 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142294 restraints weight = 28759.374| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.05 r_work: 0.3395 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 23579 Z= 0.142 Angle : 0.533 8.930 32062 Z= 0.280 Chirality : 0.043 0.184 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.723 79.396 3475 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 2.01 % Allowed : 11.67 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2934 helix: 1.99 (0.23), residues: 529 sheet: -1.11 (0.25), residues: 365 loop : -0.88 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 796 HIS 0.009 0.001 HIS E 550 PHE 0.013 0.001 PHE 2 300 TYR 0.017 0.001 TYR 2 183 ARG 0.004 0.000 ARG F 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 13) link_NAG-ASN : angle 1.40662 ( 39) link_BETA1-4 : bond 0.00222 ( 3) link_BETA1-4 : angle 1.28290 ( 9) hydrogen bonds : bond 0.03613 ( 765) hydrogen bonds : angle 5.08666 ( 2352) SS BOND : bond 0.00296 ( 93) SS BOND : angle 0.98325 ( 186) covalent geometry : bond 0.00338 (23468) covalent geometry : angle 0.52714 (31828) Misc. bond : bond 0.09988 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.7901 (mmm160) REVERT: 2 308 ASP cc_start: 0.8589 (t0) cc_final: 0.8246 (t0) REVERT: 2 337 GLN cc_start: 0.8354 (tt0) cc_final: 0.7939 (mt0) REVERT: 2 341 GLN cc_start: 0.8211 (mm110) cc_final: 0.7981 (mt0) REVERT: E 299 ASP cc_start: 0.6145 (m-30) cc_final: 0.5740 (m-30) REVERT: E 406 GLU cc_start: 0.7421 (mp0) cc_final: 0.6995 (mm-30) REVERT: E 532 HIS cc_start: 0.8559 (t-90) cc_final: 0.8336 (t70) REVERT: E 544 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7015 (tt0) REVERT: E 615 GLU cc_start: 0.7913 (mp0) cc_final: 0.7557 (mp0) REVERT: E 671 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8075 (mm) REVERT: E 745 ASP cc_start: 0.8783 (p0) cc_final: 0.8252 (p0) REVERT: E 764 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7718 (pt0) REVERT: E 820 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8042 (mt-10) REVERT: E 938 CYS cc_start: 0.6761 (m) cc_final: 0.6454 (m) REVERT: E 995 GLU cc_start: 0.7416 (tt0) cc_final: 0.7084 (tm-30) REVERT: F 167 MET cc_start: 0.6200 (mmp) cc_final: 0.5778 (ttp) REVERT: F 187 ASN cc_start: 0.8654 (t0) cc_final: 0.8006 (t0) REVERT: F 240 HIS cc_start: 0.6619 (p90) cc_final: 0.5906 (p90) REVERT: F 299 ASP cc_start: 0.7936 (m-30) cc_final: 0.7099 (m-30) REVERT: F 336 GLN cc_start: 0.7747 (mp-120) cc_final: 0.7537 (mp10) REVERT: F 446 GLU cc_start: 0.8047 (mp0) cc_final: 0.7801 (mp0) REVERT: F 649 MET cc_start: 0.8368 (mtm) cc_final: 0.8139 (mtt) REVERT: F 723 ASN cc_start: 0.8050 (t0) cc_final: 0.7834 (m-40) REVERT: F 801 HIS cc_start: 0.6965 (m-70) cc_final: 0.6708 (m90) REVERT: F 835 CYS cc_start: 0.6296 (m) cc_final: 0.6059 (m) REVERT: F 914 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7838 (mp) REVERT: F 922 TRP cc_start: 0.8061 (m100) cc_final: 0.7559 (m-10) REVERT: F 938 CYS cc_start: 0.6595 (m) cc_final: 0.6349 (m) REVERT: D 550 HIS cc_start: 0.8107 (p-80) cc_final: 0.7779 (p90) REVERT: D 622 GLN cc_start: 0.8641 (tp40) cc_final: 0.8297 (tp40) REVERT: D 825 ARG cc_start: 0.8673 (ptt180) cc_final: 0.8061 (ptt-90) REVERT: D 922 TRP cc_start: 0.8459 (m100) cc_final: 0.8230 (m100) REVERT: D 964 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: D 1004 SER cc_start: 0.8846 (t) cc_final: 0.8001 (p) REVERT: G 14 LEU cc_start: 0.8794 (tp) cc_final: 0.8432 (tp) outliers start: 49 outliers final: 27 residues processed: 295 average time/residue: 0.3312 time to fit residues: 154.1955 Evaluate side-chains 256 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 964 GLN Chi-restraints excluded: chain C residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 123 optimal weight: 0.3980 chunk 142 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS D 964 GLN G 2 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.182944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140732 restraints weight = 29248.261| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.24 r_work: 0.3359 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 23579 Z= 0.130 Angle : 0.518 9.837 32062 Z= 0.271 Chirality : 0.044 0.398 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.551 78.719 3475 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.05 % Rotamer: Outliers : 1.93 % Allowed : 12.82 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2934 helix: 2.07 (0.23), residues: 533 sheet: -1.08 (0.26), residues: 340 loop : -0.86 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 922 HIS 0.007 0.001 HIS E 550 PHE 0.012 0.001 PHE 2 300 TYR 0.015 0.001 TYR 2 183 ARG 0.004 0.000 ARG E 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 13) link_NAG-ASN : angle 2.21596 ( 39) link_BETA1-4 : bond 0.00271 ( 3) link_BETA1-4 : angle 1.32088 ( 9) hydrogen bonds : bond 0.03280 ( 765) hydrogen bonds : angle 4.83689 ( 2352) SS BOND : bond 0.00270 ( 93) SS BOND : angle 0.90266 ( 186) covalent geometry : bond 0.00311 (23468) covalent geometry : angle 0.50844 (31828) Misc. bond : bond 0.09538 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7784 (mmm160) REVERT: 2 308 ASP cc_start: 0.8435 (t0) cc_final: 0.8095 (t0) REVERT: 2 337 GLN cc_start: 0.8217 (tt0) cc_final: 0.7836 (mt0) REVERT: E 299 ASP cc_start: 0.6116 (m-30) cc_final: 0.5719 (m-30) REVERT: E 406 GLU cc_start: 0.7316 (mp0) cc_final: 0.6958 (mm-30) REVERT: E 532 HIS cc_start: 0.8527 (t-90) cc_final: 0.8291 (t70) REVERT: E 544 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7120 (tt0) REVERT: E 615 GLU cc_start: 0.7871 (mp0) cc_final: 0.7466 (mp0) REVERT: E 671 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8239 (mm) REVERT: E 745 ASP cc_start: 0.8680 (p0) cc_final: 0.8101 (p0) REVERT: E 764 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7722 (pt0) REVERT: E 820 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7978 (mt-10) REVERT: E 938 CYS cc_start: 0.6562 (m) cc_final: 0.6313 (m) REVERT: E 995 GLU cc_start: 0.7476 (tt0) cc_final: 0.7138 (tm-30) REVERT: F 167 MET cc_start: 0.6143 (mmp) cc_final: 0.5685 (ttp) REVERT: F 187 ASN cc_start: 0.8572 (t0) cc_final: 0.7955 (t0) REVERT: F 240 HIS cc_start: 0.6497 (p90) cc_final: 0.5857 (p90) REVERT: F 446 GLU cc_start: 0.8028 (mp0) cc_final: 0.7788 (mp0) REVERT: F 723 ASN cc_start: 0.7974 (t0) cc_final: 0.7740 (m-40) REVERT: F 801 HIS cc_start: 0.6971 (m-70) cc_final: 0.6738 (m90) REVERT: F 835 CYS cc_start: 0.6002 (m) cc_final: 0.5778 (m) REVERT: F 922 TRP cc_start: 0.7974 (m100) cc_final: 0.7482 (m-10) REVERT: F 938 CYS cc_start: 0.6578 (m) cc_final: 0.6295 (m) REVERT: D 825 ARG cc_start: 0.8525 (ptt180) cc_final: 0.7943 (ptt-90) REVERT: D 922 TRP cc_start: 0.8513 (m100) cc_final: 0.8240 (m100) REVERT: D 1004 SER cc_start: 0.8770 (t) cc_final: 0.7935 (p) REVERT: G 14 LEU cc_start: 0.8759 (tp) cc_final: 0.8456 (tp) outliers start: 47 outliers final: 30 residues processed: 274 average time/residue: 0.3428 time to fit residues: 149.6063 Evaluate side-chains 251 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 964 GLN Chi-restraints excluded: chain C residue 16 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 36 optimal weight: 20.0000 chunk 280 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 193 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 HIS E 353 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138467 restraints weight = 28941.981| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.24 r_work: 0.3342 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 23579 Z= 0.166 Angle : 0.532 9.306 32062 Z= 0.278 Chirality : 0.044 0.244 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.449 78.536 3475 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 2.47 % Allowed : 13.36 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2934 helix: 1.95 (0.23), residues: 533 sheet: -1.13 (0.26), residues: 335 loop : -0.87 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 PHE 0.013 0.001 PHE 2 300 TYR 0.014 0.001 TYR 2 239 ARG 0.004 0.000 ARG F 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 13) link_NAG-ASN : angle 1.83871 ( 39) link_BETA1-4 : bond 0.00241 ( 3) link_BETA1-4 : angle 1.45843 ( 9) hydrogen bonds : bond 0.03276 ( 765) hydrogen bonds : angle 4.78247 ( 2352) SS BOND : bond 0.00318 ( 93) SS BOND : angle 1.09880 ( 186) covalent geometry : bond 0.00401 (23468) covalent geometry : angle 0.52316 (31828) Misc. bond : bond 0.11375 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.7909 (mmm160) REVERT: 2 308 ASP cc_start: 0.8718 (t0) cc_final: 0.8379 (t0) REVERT: E 299 ASP cc_start: 0.6139 (m-30) cc_final: 0.5729 (m-30) REVERT: E 406 GLU cc_start: 0.7432 (mp0) cc_final: 0.7025 (mm-30) REVERT: E 532 HIS cc_start: 0.8595 (t-90) cc_final: 0.8336 (t70) REVERT: E 544 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7038 (tt0) REVERT: E 615 GLU cc_start: 0.8001 (mp0) cc_final: 0.7551 (mp0) REVERT: E 671 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8282 (mm) REVERT: E 745 ASP cc_start: 0.8879 (p0) cc_final: 0.8616 (p0) REVERT: E 764 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7822 (pt0) REVERT: E 820 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8142 (mt-10) REVERT: E 855 MET cc_start: 0.6834 (tpp) cc_final: 0.6578 (ttm) REVERT: E 995 GLU cc_start: 0.7652 (tt0) cc_final: 0.7376 (tm-30) REVERT: F 167 MET cc_start: 0.6299 (mmp) cc_final: 0.5794 (ttp) REVERT: F 187 ASN cc_start: 0.8653 (t0) cc_final: 0.8007 (t0) REVERT: F 240 HIS cc_start: 0.6683 (p90) cc_final: 0.5991 (p90) REVERT: F 723 ASN cc_start: 0.8126 (t0) cc_final: 0.7869 (m-40) REVERT: F 801 HIS cc_start: 0.7012 (m-70) cc_final: 0.6798 (m90) REVERT: F 835 CYS cc_start: 0.6668 (m) cc_final: 0.6452 (m) REVERT: F 922 TRP cc_start: 0.8129 (m100) cc_final: 0.7706 (m-10) REVERT: F 938 CYS cc_start: 0.6942 (m) cc_final: 0.6666 (m) REVERT: D 344 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: D 550 HIS cc_start: 0.8281 (p-80) cc_final: 0.7981 (p90) REVERT: D 618 HIS cc_start: 0.7426 (m-70) cc_final: 0.6712 (m170) REVERT: D 742 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.6995 (m) REVERT: D 825 ARG cc_start: 0.8682 (ptt180) cc_final: 0.8038 (ptt-90) REVERT: D 964 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: D 1004 SER cc_start: 0.8866 (t) cc_final: 0.8055 (p) REVERT: C 56 LYS cc_start: 0.8188 (tttt) cc_final: 0.7617 (mmtt) REVERT: C 126 ASP cc_start: 0.9032 (t70) cc_final: 0.8802 (t0) REVERT: G 14 LEU cc_start: 0.8790 (tp) cc_final: 0.8531 (tp) outliers start: 60 outliers final: 42 residues processed: 278 average time/residue: 0.3292 time to fit residues: 145.2831 Evaluate side-chains 261 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 760 LEU Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 964 GLN Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS D 876 ASN D 964 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137493 restraints weight = 28804.814| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.21 r_work: 0.3327 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 23579 Z= 0.184 Angle : 0.540 9.084 32062 Z= 0.283 Chirality : 0.044 0.223 3407 Planarity : 0.004 0.050 4125 Dihedral : 5.382 78.980 3475 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 3.04 % Allowed : 13.73 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 2934 helix: 1.89 (0.22), residues: 536 sheet: -1.23 (0.26), residues: 335 loop : -0.90 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 PHE 0.014 0.001 PHE 2 280 TYR 0.016 0.001 TYR 2 239 ARG 0.004 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 13) link_NAG-ASN : angle 1.74443 ( 39) link_BETA1-4 : bond 0.00257 ( 3) link_BETA1-4 : angle 1.52473 ( 9) hydrogen bonds : bond 0.03302 ( 765) hydrogen bonds : angle 4.79343 ( 2352) SS BOND : bond 0.00359 ( 93) SS BOND : angle 1.10654 ( 186) covalent geometry : bond 0.00443 (23468) covalent geometry : angle 0.53169 (31828) Misc. bond : bond 0.12066 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 238 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.7908 (mmm160) REVERT: 2 308 ASP cc_start: 0.8780 (t0) cc_final: 0.8488 (t0) REVERT: E 299 ASP cc_start: 0.6123 (m-30) cc_final: 0.5707 (m-30) REVERT: E 406 GLU cc_start: 0.7461 (mp0) cc_final: 0.7011 (mm-30) REVERT: E 466 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6186 (pm20) REVERT: E 532 HIS cc_start: 0.8609 (t-90) cc_final: 0.8332 (t70) REVERT: E 544 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7068 (tt0) REVERT: E 671 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8366 (mm) REVERT: E 745 ASP cc_start: 0.8877 (p0) cc_final: 0.8617 (p0) REVERT: E 764 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7898 (pt0) REVERT: E 820 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8214 (mt-10) REVERT: E 995 GLU cc_start: 0.7716 (tt0) cc_final: 0.7423 (tm-30) REVERT: F 167 MET cc_start: 0.6377 (mmp) cc_final: 0.5851 (ttp) REVERT: F 240 HIS cc_start: 0.6744 (p90) cc_final: 0.6063 (p90) REVERT: F 645 ILE cc_start: 0.7970 (mm) cc_final: 0.7567 (pt) REVERT: F 723 ASN cc_start: 0.8107 (t0) cc_final: 0.7853 (m-40) REVERT: F 922 TRP cc_start: 0.8167 (m100) cc_final: 0.7787 (m100) REVERT: F 938 CYS cc_start: 0.6992 (m) cc_final: 0.6720 (m) REVERT: D 344 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.6927 (mp10) REVERT: D 543 GLU cc_start: 0.8276 (tt0) cc_final: 0.8071 (tt0) REVERT: D 550 HIS cc_start: 0.8255 (p-80) cc_final: 0.7935 (p90) REVERT: D 618 HIS cc_start: 0.7391 (m-70) cc_final: 0.6753 (m170) REVERT: D 742 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7390 (m) REVERT: D 825 ARG cc_start: 0.8680 (ptt180) cc_final: 0.8043 (ptt-90) REVERT: D 1004 SER cc_start: 0.8850 (t) cc_final: 0.8036 (p) REVERT: C 56 LYS cc_start: 0.8110 (tttt) cc_final: 0.7564 (mmtt) REVERT: C 126 ASP cc_start: 0.9013 (t70) cc_final: 0.8794 (t0) REVERT: G 14 LEU cc_start: 0.8739 (tp) cc_final: 0.8531 (tp) outliers start: 74 outliers final: 50 residues processed: 295 average time/residue: 0.3305 time to fit residues: 155.4853 Evaluate side-chains 275 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 443 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 876 ASN Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 172 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 187 ASN D 240 HIS D 475 HIS D 876 ASN D 964 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.179250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137705 restraints weight = 28923.359| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.16 r_work: 0.3318 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 23579 Z= 0.189 Angle : 0.550 9.040 32062 Z= 0.286 Chirality : 0.044 0.212 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.367 79.221 3475 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 3.21 % Allowed : 14.30 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2934 helix: 1.86 (0.22), residues: 536 sheet: -1.27 (0.26), residues: 343 loop : -0.93 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 14 HIS 0.007 0.001 HIS E 550 PHE 0.014 0.001 PHE 2 280 TYR 0.016 0.001 TYR 2 239 ARG 0.007 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 13) link_NAG-ASN : angle 1.69851 ( 39) link_BETA1-4 : bond 0.00290 ( 3) link_BETA1-4 : angle 1.51944 ( 9) hydrogen bonds : bond 0.03312 ( 765) hydrogen bonds : angle 4.78141 ( 2352) SS BOND : bond 0.00366 ( 93) SS BOND : angle 1.16879 ( 186) covalent geometry : bond 0.00456 (23468) covalent geometry : angle 0.54051 (31828) Misc. bond : bond 0.11987 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 233 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.7927 (mmm160) REVERT: 2 308 ASP cc_start: 0.8813 (t0) cc_final: 0.8533 (t0) REVERT: E 299 ASP cc_start: 0.6160 (m-30) cc_final: 0.5756 (m-30) REVERT: E 406 GLU cc_start: 0.7449 (mp0) cc_final: 0.7032 (mm-30) REVERT: E 466 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: E 532 HIS cc_start: 0.8606 (t-90) cc_final: 0.8360 (t70) REVERT: E 544 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7079 (tt0) REVERT: E 615 GLU cc_start: 0.8052 (mp0) cc_final: 0.7711 (mp0) REVERT: E 671 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8352 (mm) REVERT: E 745 ASP cc_start: 0.8918 (p0) cc_final: 0.8652 (p0) REVERT: E 764 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7912 (pt0) REVERT: E 820 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8304 (mt-10) REVERT: E 855 MET cc_start: 0.7283 (ttm) cc_final: 0.7038 (ttm) REVERT: E 995 GLU cc_start: 0.7718 (tt0) cc_final: 0.7449 (tm-30) REVERT: F 167 MET cc_start: 0.6508 (mmp) cc_final: 0.5983 (ttp) REVERT: F 240 HIS cc_start: 0.6769 (p90) cc_final: 0.6103 (p90) REVERT: F 645 ILE cc_start: 0.7912 (mm) cc_final: 0.7536 (pt) REVERT: F 723 ASN cc_start: 0.8140 (t0) cc_final: 0.7900 (m-40) REVERT: F 785 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7517 (mm-30) REVERT: F 922 TRP cc_start: 0.8190 (m100) cc_final: 0.7885 (m100) REVERT: F 938 CYS cc_start: 0.7058 (m) cc_final: 0.6786 (m) REVERT: D 344 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: D 550 HIS cc_start: 0.8291 (p-80) cc_final: 0.7982 (p90) REVERT: D 580 TYR cc_start: 0.8622 (p90) cc_final: 0.8123 (p90) REVERT: D 618 HIS cc_start: 0.7403 (m-70) cc_final: 0.6773 (m170) REVERT: D 736 HIS cc_start: 0.4876 (OUTLIER) cc_final: 0.4293 (p-80) REVERT: D 742 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7409 (m) REVERT: D 825 ARG cc_start: 0.8704 (ptt180) cc_final: 0.8093 (ptt-90) REVERT: D 922 TRP cc_start: 0.8550 (m100) cc_final: 0.8234 (m100) REVERT: D 1004 SER cc_start: 0.8759 (t) cc_final: 0.7968 (p) REVERT: C 56 LYS cc_start: 0.8145 (tttt) cc_final: 0.7598 (mmtt) REVERT: C 126 ASP cc_start: 0.9004 (t70) cc_final: 0.8793 (t0) REVERT: G 14 LEU cc_start: 0.8799 (tp) cc_final: 0.8572 (tp) outliers start: 78 outliers final: 52 residues processed: 291 average time/residue: 0.3497 time to fit residues: 161.9233 Evaluate side-chains 280 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 82 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 247 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 291 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 HIS E 723 ASN F 648 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.179220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142032 restraints weight = 28840.541| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.16 r_work: 0.3351 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 23579 Z= 0.124 Angle : 0.506 8.996 32062 Z= 0.266 Chirality : 0.043 0.214 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.124 79.596 3475 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 2.47 % Allowed : 15.21 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2934 helix: 2.11 (0.23), residues: 537 sheet: -1.19 (0.26), residues: 343 loop : -0.87 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 14 HIS 0.007 0.001 HIS F 736 PHE 0.011 0.001 PHE 2 300 TYR 0.023 0.001 TYR 2 183 ARG 0.008 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 13) link_NAG-ASN : angle 1.52427 ( 39) link_BETA1-4 : bond 0.00244 ( 3) link_BETA1-4 : angle 1.27059 ( 9) hydrogen bonds : bond 0.03009 ( 765) hydrogen bonds : angle 4.55871 ( 2352) SS BOND : bond 0.00263 ( 93) SS BOND : angle 0.93511 ( 186) covalent geometry : bond 0.00300 (23468) covalent geometry : angle 0.49999 (31828) Misc. bond : bond 0.08584 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.7925 (mmm160) REVERT: 2 308 ASP cc_start: 0.8793 (t0) cc_final: 0.8518 (t0) REVERT: E 299 ASP cc_start: 0.6175 (m-30) cc_final: 0.5761 (m-30) REVERT: E 376 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7570 (ttp-110) REVERT: E 406 GLU cc_start: 0.7403 (mp0) cc_final: 0.6873 (mp0) REVERT: E 408 ASP cc_start: 0.8038 (t0) cc_final: 0.7566 (t0) REVERT: E 466 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: E 532 HIS cc_start: 0.8581 (t-90) cc_final: 0.8320 (t70) REVERT: E 544 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7028 (tt0) REVERT: E 671 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8308 (mm) REVERT: E 745 ASP cc_start: 0.8888 (p0) cc_final: 0.8608 (p0) REVERT: E 764 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7796 (pt0) REVERT: E 820 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8325 (mt-10) REVERT: E 855 MET cc_start: 0.7194 (ttm) cc_final: 0.6991 (ttm) REVERT: E 995 GLU cc_start: 0.7725 (tt0) cc_final: 0.7485 (tm-30) REVERT: F 167 MET cc_start: 0.6458 (mmp) cc_final: 0.5973 (ttp) REVERT: F 187 ASN cc_start: 0.8649 (t0) cc_final: 0.7849 (t0) REVERT: F 226 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.6541 (mt) REVERT: F 240 HIS cc_start: 0.6715 (p90) cc_final: 0.6238 (p90) REVERT: F 645 ILE cc_start: 0.7889 (mm) cc_final: 0.7520 (pt) REVERT: F 723 ASN cc_start: 0.8158 (t0) cc_final: 0.7883 (m-40) REVERT: F 785 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7288 (mm-30) REVERT: F 801 HIS cc_start: 0.7198 (m90) cc_final: 0.6831 (m90) REVERT: F 922 TRP cc_start: 0.8148 (m100) cc_final: 0.7848 (m100) REVERT: F 938 CYS cc_start: 0.7047 (m) cc_final: 0.6786 (m) REVERT: D 344 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: D 550 HIS cc_start: 0.8263 (p-80) cc_final: 0.8021 (p90) REVERT: D 618 HIS cc_start: 0.7338 (m-70) cc_final: 0.6778 (m170) REVERT: D 736 HIS cc_start: 0.4732 (OUTLIER) cc_final: 0.4215 (p-80) REVERT: D 742 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7240 (m) REVERT: D 825 ARG cc_start: 0.8679 (ptt180) cc_final: 0.8187 (ptt-90) REVERT: D 922 TRP cc_start: 0.8477 (m100) cc_final: 0.8228 (m100) REVERT: D 1004 SER cc_start: 0.8754 (t) cc_final: 0.7946 (p) REVERT: C 56 LYS cc_start: 0.8111 (tttt) cc_final: 0.7597 (mmtt) REVERT: G 14 LEU cc_start: 0.8784 (tp) cc_final: 0.8581 (tp) outliers start: 60 outliers final: 48 residues processed: 284 average time/residue: 0.3363 time to fit residues: 151.7248 Evaluate side-chains 279 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 172 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.177810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139260 restraints weight = 29010.609| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.34 r_work: 0.3264 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.176 23579 Z= 0.231 Angle : 0.573 6.947 32062 Z= 0.300 Chirality : 0.045 0.220 3407 Planarity : 0.004 0.050 4125 Dihedral : 5.354 80.935 3475 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 2.79 % Allowed : 15.54 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2934 helix: 1.86 (0.22), residues: 535 sheet: -1.33 (0.25), residues: 358 loop : -0.91 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 14 HIS 0.008 0.001 HIS G 63 PHE 0.017 0.001 PHE 2 280 TYR 0.024 0.002 TYR 2 183 ARG 0.008 0.001 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 13) link_NAG-ASN : angle 1.75379 ( 39) link_BETA1-4 : bond 0.00275 ( 3) link_BETA1-4 : angle 1.63383 ( 9) hydrogen bonds : bond 0.03376 ( 765) hydrogen bonds : angle 4.80400 ( 2352) SS BOND : bond 0.00429 ( 93) SS BOND : angle 1.17804 ( 186) covalent geometry : bond 0.00555 (23468) covalent geometry : angle 0.56354 (31828) Misc. bond : bond 0.12988 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7807 (mmm160) REVERT: 2 308 ASP cc_start: 0.8622 (t0) cc_final: 0.8352 (t0) REVERT: E 299 ASP cc_start: 0.6256 (m-30) cc_final: 0.5888 (m-30) REVERT: E 406 GLU cc_start: 0.7342 (mp0) cc_final: 0.6872 (mp0) REVERT: E 439 LEU cc_start: 0.8998 (mt) cc_final: 0.8687 (mp) REVERT: E 466 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: E 532 HIS cc_start: 0.8587 (t-90) cc_final: 0.8335 (t70) REVERT: E 544 GLU cc_start: 0.7753 (tm-30) cc_final: 0.6959 (tt0) REVERT: E 671 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8366 (mm) REVERT: E 745 ASP cc_start: 0.8862 (p0) cc_final: 0.8581 (p0) REVERT: E 764 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7878 (pt0) REVERT: E 855 MET cc_start: 0.7220 (ttm) cc_final: 0.7014 (ttm) REVERT: F 167 MET cc_start: 0.6394 (mmp) cc_final: 0.5995 (ttp) REVERT: F 187 ASN cc_start: 0.8579 (t0) cc_final: 0.7778 (t0) REVERT: F 226 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.6541 (mt) REVERT: F 240 HIS cc_start: 0.6655 (p90) cc_final: 0.6055 (p90) REVERT: F 785 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7445 (mm-30) REVERT: F 938 CYS cc_start: 0.6684 (m) cc_final: 0.6392 (m) REVERT: D 344 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: D 550 HIS cc_start: 0.8169 (p-80) cc_final: 0.7856 (p90) REVERT: D 580 TYR cc_start: 0.8535 (p90) cc_final: 0.7876 (p90) REVERT: D 618 HIS cc_start: 0.7305 (m-70) cc_final: 0.6718 (m170) REVERT: D 736 HIS cc_start: 0.4905 (OUTLIER) cc_final: 0.4302 (p-80) REVERT: D 742 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7684 (m) REVERT: D 825 ARG cc_start: 0.8534 (ptt180) cc_final: 0.7941 (ptt-90) REVERT: D 922 TRP cc_start: 0.8467 (m100) cc_final: 0.8119 (m100) REVERT: D 1004 SER cc_start: 0.8683 (t) cc_final: 0.7938 (p) REVERT: C 56 LYS cc_start: 0.8003 (tttt) cc_final: 0.7554 (mmtt) REVERT: C 126 ASP cc_start: 0.8742 (t70) cc_final: 0.8481 (t0) REVERT: G 14 LEU cc_start: 0.8757 (tp) cc_final: 0.8546 (tp) outliers start: 68 outliers final: 54 residues processed: 284 average time/residue: 0.3352 time to fit residues: 151.8134 Evaluate side-chains 271 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 225 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 171 optimal weight: 0.1980 chunk 223 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 150 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 187 ASN D 240 HIS D 475 HIS D 754 HIS G 2 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.178610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141268 restraints weight = 28997.809| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.09 r_work: 0.3356 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 23579 Z= 0.129 Angle : 0.529 10.870 32062 Z= 0.277 Chirality : 0.043 0.192 3407 Planarity : 0.004 0.054 4125 Dihedral : 5.147 80.098 3475 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 2.63 % Allowed : 15.87 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2934 helix: 2.09 (0.23), residues: 537 sheet: -1.24 (0.26), residues: 333 loop : -0.87 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 748 HIS 0.006 0.001 HIS E 550 PHE 0.011 0.001 PHE 2 300 TYR 0.024 0.001 TYR 2 183 ARG 0.008 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 13) link_NAG-ASN : angle 1.55543 ( 39) link_BETA1-4 : bond 0.00234 ( 3) link_BETA1-4 : angle 1.32880 ( 9) hydrogen bonds : bond 0.03063 ( 765) hydrogen bonds : angle 4.61422 ( 2352) SS BOND : bond 0.00259 ( 93) SS BOND : angle 0.94182 ( 186) covalent geometry : bond 0.00310 (23468) covalent geometry : angle 0.52291 (31828) Misc. bond : bond 0.08703 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.7888 (mmm160) REVERT: 2 308 ASP cc_start: 0.8822 (t0) cc_final: 0.8556 (t0) REVERT: E 299 ASP cc_start: 0.6222 (m-30) cc_final: 0.5846 (m-30) REVERT: E 376 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7618 (ttp-110) REVERT: E 406 GLU cc_start: 0.7415 (mp0) cc_final: 0.6881 (mp0) REVERT: E 408 ASP cc_start: 0.8033 (t0) cc_final: 0.7554 (t0) REVERT: E 439 LEU cc_start: 0.9027 (mt) cc_final: 0.8696 (mp) REVERT: E 463 ASP cc_start: 0.5256 (p0) cc_final: 0.4816 (t0) REVERT: E 466 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: E 532 HIS cc_start: 0.8609 (t-90) cc_final: 0.8354 (t70) REVERT: E 544 GLU cc_start: 0.7699 (tm-30) cc_final: 0.6925 (tt0) REVERT: E 615 GLU cc_start: 0.7880 (mp0) cc_final: 0.7628 (mp0) REVERT: E 671 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8366 (mm) REVERT: E 745 ASP cc_start: 0.8868 (p0) cc_final: 0.8593 (p0) REVERT: E 764 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7823 (pt0) REVERT: F 167 MET cc_start: 0.6519 (mmp) cc_final: 0.5995 (ttp) REVERT: F 187 ASN cc_start: 0.8648 (t0) cc_final: 0.7857 (t0) REVERT: F 226 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6439 (mt) REVERT: F 240 HIS cc_start: 0.6759 (p90) cc_final: 0.6157 (p90) REVERT: F 352 LYS cc_start: 0.7759 (tttm) cc_final: 0.6755 (mmtm) REVERT: F 625 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7058 (mmmt) REVERT: F 785 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7503 (mm-30) REVERT: F 913 ARG cc_start: 0.7246 (ptt90) cc_final: 0.6962 (ptt-90) REVERT: F 922 TRP cc_start: 0.8013 (m100) cc_final: 0.7770 (m-10) REVERT: F 938 CYS cc_start: 0.7050 (m) cc_final: 0.6782 (m) REVERT: D 344 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: D 550 HIS cc_start: 0.8275 (p-80) cc_final: 0.7996 (p90) REVERT: D 580 TYR cc_start: 0.8563 (p90) cc_final: 0.8030 (p90) REVERT: D 593 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7381 (pp20) REVERT: D 618 HIS cc_start: 0.7288 (m-70) cc_final: 0.6773 (m170) REVERT: D 736 HIS cc_start: 0.4858 (OUTLIER) cc_final: 0.4379 (p-80) REVERT: D 742 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7562 (m) REVERT: D 825 ARG cc_start: 0.8639 (ptt180) cc_final: 0.8074 (ptt-90) REVERT: D 922 TRP cc_start: 0.8386 (m100) cc_final: 0.8157 (m100) REVERT: D 1004 SER cc_start: 0.8768 (t) cc_final: 0.7980 (p) REVERT: C 56 LYS cc_start: 0.8082 (tttt) cc_final: 0.7558 (mmtt) outliers start: 64 outliers final: 51 residues processed: 276 average time/residue: 0.3365 time to fit residues: 146.1970 Evaluate side-chains 276 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 171 LEU Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 87 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 283 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 255 optimal weight: 0.0470 chunk 47 optimal weight: 0.0870 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 240 HIS D 241 GLN D 327 HIS D 464 HIS D 475 HIS ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.180867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144328 restraints weight = 28839.476| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.07 r_work: 0.3392 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23579 Z= 0.105 Angle : 0.511 9.498 32062 Z= 0.268 Chirality : 0.042 0.172 3407 Planarity : 0.004 0.069 4125 Dihedral : 4.999 79.297 3475 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 2.22 % Allowed : 16.19 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2934 helix: 2.29 (0.23), residues: 537 sheet: -1.14 (0.26), residues: 338 loop : -0.82 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 455 HIS 0.017 0.001 HIS D 240 PHE 0.021 0.001 PHE F 176 TYR 0.024 0.001 TYR 2 183 ARG 0.008 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 13) link_NAG-ASN : angle 1.39730 ( 39) link_BETA1-4 : bond 0.00273 ( 3) link_BETA1-4 : angle 1.15377 ( 9) hydrogen bonds : bond 0.02873 ( 765) hydrogen bonds : angle 4.43620 ( 2352) SS BOND : bond 0.00207 ( 93) SS BOND : angle 0.84046 ( 186) covalent geometry : bond 0.00249 (23468) covalent geometry : angle 0.50604 (31828) Misc. bond : bond 0.05653 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14112.73 seconds wall clock time: 244 minutes 5.38 seconds (14645.38 seconds total)