Starting phenix.real_space_refine on Fri Mar 6 21:25:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7knh_22949/03_2026/7knh_22949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7knh_22949/03_2026/7knh_22949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7knh_22949/03_2026/7knh_22949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7knh_22949/03_2026/7knh_22949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7knh_22949/03_2026/7knh_22949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7knh_22949/03_2026/7knh_22949.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 167 5.16 5 C 21929 2.51 5 N 5632 2.21 5 O 6655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 190 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34383 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7837 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8020 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8018 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.44, per 1000 atoms: 0.25 Number of scatterers: 34383 At special positions: 0 Unit cell: (137.54, 161.874, 244.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 167 16.00 O 6655 8.00 N 5632 7.00 C 21929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG A1314 " - " ASN A 603 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG B1314 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 657 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 322 " " NAG D 703 " - " ASN D 432 " " NAG D 704 " - " ASN D 49 " " NAG E 701 " - " ASN E 432 " " NAG E 702 " - " ASN E 103 " " NAG E 703 " - " ASN E 90 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 343 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 717 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 43 sheets defined 35.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.317A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.853A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.220A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.643A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.598A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.840A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.455A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 4.200A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.942A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.731A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.877A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.914A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.527A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.680A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.522A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.813A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.582A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.814A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.577A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.514A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.677A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.581A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.622A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.169A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.964A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.529A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 removed outlier: 3.648A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 73 " --> pdb=" O TRP E 69 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 removed outlier: 3.827A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 4.646A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 154 removed outlier: 4.231A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.704A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.582A pdb=" N GLN E 175 " --> pdb=" O VAL E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 176 through 187 removed outlier: 3.830A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.620A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 245 removed outlier: 3.859A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.750A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.845A pdb=" N LEU E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 267 " --> pdb=" O ALA E 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 263 through 267' Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.430A pdb=" N LEU E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.876A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.593A pdb=" N GLU E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.671A pdb=" N MET E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY E 377 " --> pdb=" O HIS E 373 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.996A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 432 through 447 removed outlier: 4.122A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.454A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.634A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 523 removed outlier: 4.074A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 533 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.597A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 3.516A pdb=" N SER E 563 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 560 through 564' Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.648A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 removed outlier: 4.335A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 581 through 586' Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.715A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 598 " --> pdb=" O TRP E 594 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.607A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.725A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.819A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.718A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.699A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.007A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.512A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.652A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.806A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 951 Processing helix chain 'B' and resid 952 through 967 removed outlier: 3.809A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.547A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.968A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.181A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.571A pdb=" N ASP D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 4.010A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.549A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 4.595A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.262A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.606A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.590A pdb=" N GLN D 175 " --> pdb=" O VAL D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.626A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.830A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 249 removed outlier: 3.607A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.722A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 247 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.864A pdb=" N LEU D 266 " --> pdb=" O PRO D 263 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU D 267 " --> pdb=" O ALA D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.678A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.792A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.574A pdb=" N PHE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.103A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.535A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.503A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.553A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.069A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.906A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.642A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.447A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 586' Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.828A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.835A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.728A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 578 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.299A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.588A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 189 through 190 Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.300A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.686A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.795A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.567A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.567A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.653A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.653A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.141A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1086 through 1088 Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.727A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 201 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.160A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.525A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.154A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 378 through 380 removed outlier: 3.694A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.507A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.750A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 565 through 569 removed outlier: 6.294A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.396A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.218A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 712 through 723 removed outlier: 6.961A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AC9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.334A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.510A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD3, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.055A pdb=" N ALA E 348 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU E 359 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASP E 350 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG E 357 " --> pdb=" O ASP E 350 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY E 352 " --> pdb=" O ASP E 355 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.689A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.982A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.644A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.687A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.894A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.843A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.676A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 723 removed outlier: 6.443A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AE4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.724A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.637A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.435A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.69 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9763 1.33 - 1.46: 8248 1.46 - 1.58: 16950 1.58 - 1.71: 0 1.71 - 1.83: 237 Bond restraints: 35198 Sorted by residual: bond pdb=" N VAL A 534 " pdb=" CA VAL A 534 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.99e+00 bond pdb=" CG PRO D 258 " pdb=" CD PRO D 258 " ideal model delta sigma weight residual 1.503 1.403 0.100 3.40e-02 8.65e+02 8.72e+00 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.20e+00 bond pdb=" N ILE E 54 " pdb=" CA ILE E 54 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.22e+00 bond pdb=" N TRP D 473 " pdb=" CA TRP D 473 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.20e+00 ... (remaining 35193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 46980 2.41 - 4.81: 776 4.81 - 7.22: 88 7.22 - 9.62: 24 9.62 - 12.03: 6 Bond angle restraints: 47874 Sorted by residual: angle pdb=" CA THR A 531 " pdb=" CB THR A 531 " pdb=" OG1 THR A 531 " ideal model delta sigma weight residual 109.60 99.45 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" CB PRO A 330 " ideal model delta sigma weight residual 103.25 97.36 5.89 1.05e+00 9.07e-01 3.14e+01 angle pdb=" C VAL A 534 " pdb=" N LYS A 535 " pdb=" CA LYS A 535 " ideal model delta sigma weight residual 122.81 115.18 7.63 1.57e+00 4.06e-01 2.36e+01 angle pdb=" N PRO D 258 " pdb=" CD PRO D 258 " pdb=" CG PRO D 258 " ideal model delta sigma weight residual 103.20 95.96 7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" C PRO A 330 " pdb=" CA PRO A 330 " pdb=" CB PRO A 330 " ideal model delta sigma weight residual 111.56 103.93 7.63 1.65e+00 3.67e-01 2.14e+01 ... (remaining 47869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 19453 17.99 - 35.99: 1758 35.99 - 53.98: 327 53.98 - 71.97: 75 71.97 - 89.97: 37 Dihedral angle restraints: 21650 sinusoidal: 9218 harmonic: 12432 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.00 -88.00 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 22.47 70.53 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.49 64.49 1 1.00e+01 1.00e-02 5.47e+01 ... (remaining 21647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4684 0.069 - 0.138: 752 0.138 - 0.206: 44 0.206 - 0.275: 8 0.275 - 0.344: 4 Chirality restraints: 5492 Sorted by residual: chirality pdb=" C1 NAG D 703 " pdb=" ND2 ASN D 432 " pdb=" C2 NAG D 703 " pdb=" O5 NAG D 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ARG A 328 " pdb=" N ARG A 328 " pdb=" C ARG A 328 " pdb=" CB ARG A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 5489 not shown) Planarity restraints: 6174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.341 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A1301 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 703 " 0.292 2.00e-02 2.50e+03 2.45e-01 7.50e+02 pdb=" C7 NAG D 703 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG D 703 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG D 703 " -0.417 2.00e-02 2.50e+03 pdb=" O7 NAG D 703 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 704 " -0.216 2.00e-02 2.50e+03 1.80e-01 4.03e+02 pdb=" C7 NAG D 704 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG D 704 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG D 704 " 0.295 2.00e-02 2.50e+03 pdb=" O7 NAG D 704 " 0.017 2.00e-02 2.50e+03 ... (remaining 6171 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 791 2.69 - 3.24: 33089 3.24 - 3.80: 52255 3.80 - 4.35: 67536 4.35 - 4.90: 109594 Nonbonded interactions: 263265 Sorted by model distance: nonbonded pdb=" O THR E 548 " pdb=" NE2 GLN E 552 " model vdw 2.139 3.120 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN E 388 " pdb=" OG SER E 563 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASN C 394 " pdb=" OH TYR A 200 " model vdw 2.236 3.040 ... (remaining 263260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 141 o \ r resid 156 through 176 or (resid 187 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 194 or (resid 195 through 198 an \ d (name N or name CA or name C or name O or name CB )) or resid 199 or (resid 20 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 201 through \ 243 or resid 264 through 620 or resid 640 through 811 or resid 815 through 828 o \ r resid 853 through 1147 or resid 1302 through 1314)) selection = (chain 'B' and (resid 26 through 66 or resid 81 through 141 or resid 156 through \ 176 or (resid 187 through 188 and (name N or name CA or name C or name O or nam \ e CB )) or resid 189 through 194 or (resid 195 through 198 and (name N or name C \ A or name C or name O or name CB )) or resid 199 or (resid 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 243 or resid 264 th \ rough 620 or resid 640 through 811 or resid 815 through 828 or resid 853 through \ 1147 or resid 1302 through 1314)) selection = (chain 'C' and (resid 26 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 134 o \ r (resid 135 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 36 through 163 or (resid 164 and (name N or name CA or name C or name O or name \ CB )) or resid 165 through 189 or (resid 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 289 o \ r (resid 290 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 91 through 620 or resid 640 through 676 or resid 690 through 1313)) } ncs_group { reference = (chain 'D' and resid 19 through 703) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.980 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.004 0.100 35299 Z= 0.191 Angle : 0.754 21.604 48132 Z= 0.407 Chirality : 0.049 0.344 5492 Planarity : 0.007 0.292 6122 Dihedral : 14.124 89.966 13503 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 0.13 % Allowed : 0.70 % Favored : 99.16 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.12), residues: 4206 helix: -1.59 (0.13), residues: 1229 sheet: 0.19 (0.24), residues: 502 loop : -1.19 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 115 TYR 0.031 0.001 TYR E 196 PHE 0.025 0.001 PHE D 592 TRP 0.065 0.001 TRP E 168 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00367 (35198) covalent geometry : angle 0.73584 (47874) SS BOND : bond 0.00221 ( 45) SS BOND : angle 1.01607 ( 90) hydrogen bonds : bond 0.30797 ( 1143) hydrogen bonds : angle 9.13969 ( 3213) link_BETA1-4 : bond 0.00409 ( 4) link_BETA1-4 : angle 1.14218 ( 12) link_NAG-ASN : bond 0.00449 ( 52) link_NAG-ASN : angle 2.93704 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 ASN cc_start: 0.7685 (m-40) cc_final: 0.7060 (p0) REVERT: A 153 MET cc_start: 0.3333 (ptt) cc_final: 0.3030 (pmm) REVERT: A 312 ILE cc_start: 0.8461 (pt) cc_final: 0.8246 (pt) REVERT: A 779 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7984 (tm-30) REVERT: E 111 ASP cc_start: 0.7954 (t0) cc_final: 0.7139 (p0) REVERT: E 297 MET cc_start: -0.0732 (mpp) cc_final: -0.0978 (mpp) REVERT: E 462 MET cc_start: 0.0592 (ptm) cc_final: 0.0290 (mmp) REVERT: B 452 LEU cc_start: 0.8347 (mp) cc_final: 0.8082 (mp) REVERT: B 697 MET cc_start: 0.7597 (tpp) cc_final: 0.7270 (tpp) REVERT: D 123 MET cc_start: 0.2805 (ttm) cc_final: 0.2558 (tpt) REVERT: D 177 ARG cc_start: 0.7344 (tpt90) cc_final: 0.6885 (ptt90) outliers start: 5 outliers final: 0 residues processed: 198 average time/residue: 0.2003 time to fit residues: 68.5047 Evaluate side-chains 138 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 422 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN E 552 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 949 GLN B1011 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 442 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.119891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077510 restraints weight = 153839.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078033 restraints weight = 73048.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.074335 restraints weight = 42338.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.074479 restraints weight = 31260.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074753 restraints weight = 24317.446| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 35299 Z= 0.299 Angle : 0.741 16.641 48132 Z= 0.376 Chirality : 0.048 0.374 5492 Planarity : 0.005 0.066 6122 Dihedral : 6.612 59.294 5731 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.57 % Allowed : 8.55 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.12), residues: 4206 helix: -0.64 (0.13), residues: 1282 sheet: -0.32 (0.22), residues: 550 loop : -1.22 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 115 TYR 0.029 0.002 TYR A1067 PHE 0.032 0.002 PHE B1089 TRP 0.025 0.002 TRP E 168 HIS 0.008 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00650 (35198) covalent geometry : angle 0.72136 (47874) SS BOND : bond 0.00497 ( 45) SS BOND : angle 1.36110 ( 90) hydrogen bonds : bond 0.05226 ( 1143) hydrogen bonds : angle 6.04487 ( 3213) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 1.66865 ( 12) link_NAG-ASN : bond 0.00521 ( 52) link_NAG-ASN : angle 2.89837 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 490 PHE cc_start: 0.8516 (t80) cc_final: 0.8156 (t80) REVERT: A 153 MET cc_start: 0.3552 (ptt) cc_final: 0.3323 (pmm) REVERT: A 779 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 954 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: E 62 MET cc_start: 0.3700 (mmm) cc_final: 0.3466 (mmp) REVERT: E 111 ASP cc_start: 0.7913 (t0) cc_final: 0.7682 (p0) REVERT: E 297 MET cc_start: 0.0398 (mpp) cc_final: 0.0136 (mpp) REVERT: E 474 MET cc_start: 0.6350 (mmp) cc_final: 0.4660 (mtt) REVERT: B 697 MET cc_start: 0.8736 (tpp) cc_final: 0.8201 (tpp) REVERT: B 1050 MET cc_start: 0.8379 (ptt) cc_final: 0.8129 (ptt) REVERT: D 82 MET cc_start: 0.7411 (mpp) cc_final: 0.6386 (pmm) REVERT: D 323 MET cc_start: 0.4494 (tpt) cc_final: 0.4181 (tpt) REVERT: D 332 MET cc_start: 0.6208 (ppp) cc_final: 0.5667 (pmm) REVERT: D 462 MET cc_start: 0.6677 (mmt) cc_final: 0.6024 (ppp) REVERT: D 474 MET cc_start: 0.3612 (mmm) cc_final: 0.2161 (mmm) REVERT: D 476 LYS cc_start: 0.3050 (tttp) cc_final: 0.2838 (mtpp) outliers start: 21 outliers final: 13 residues processed: 168 average time/residue: 0.1900 time to fit residues: 55.2383 Evaluate side-chains 137 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 70 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 371 optimal weight: 0.0370 chunk 402 optimal weight: 40.0000 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 254 optimal weight: 0.4980 chunk 250 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 422 ASN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN D 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.123021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.082336 restraints weight = 173203.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.083062 restraints weight = 85923.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.082111 restraints weight = 46457.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082223 restraints weight = 46734.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.082099 restraints weight = 39916.366| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35299 Z= 0.117 Angle : 0.558 16.935 48132 Z= 0.278 Chirality : 0.044 0.321 5492 Planarity : 0.004 0.058 6122 Dihedral : 5.806 58.489 5731 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.76 % Allowed : 11.33 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4206 helix: 0.10 (0.14), residues: 1262 sheet: -0.27 (0.22), residues: 539 loop : -1.18 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.025 0.001 TYR C 449 PHE 0.038 0.001 PHE C 392 TRP 0.015 0.001 TRP E 168 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00246 (35198) covalent geometry : angle 0.53932 (47874) SS BOND : bond 0.00215 ( 45) SS BOND : angle 0.91112 ( 90) hydrogen bonds : bond 0.04648 ( 1143) hydrogen bonds : angle 5.49065 ( 3213) link_BETA1-4 : bond 0.00380 ( 4) link_BETA1-4 : angle 1.09205 ( 12) link_NAG-ASN : bond 0.00427 ( 52) link_NAG-ASN : angle 2.51910 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 515 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8603 (t80) REVERT: C 1005 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8759 (tp40) REVERT: A 153 MET cc_start: 0.4146 (ptt) cc_final: 0.3540 (pmm) REVERT: A 779 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 980 ILE cc_start: 0.9220 (mm) cc_final: 0.9019 (tp) REVERT: E 49 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.6828 (t0) REVERT: E 62 MET cc_start: 0.2460 (mmm) cc_final: 0.1817 (mmm) REVERT: E 111 ASP cc_start: 0.7845 (t0) cc_final: 0.7549 (p0) REVERT: E 474 MET cc_start: 0.5894 (mmp) cc_final: 0.3885 (mtt) REVERT: E 579 MET cc_start: -0.2701 (mmt) cc_final: -0.3807 (mmm) REVERT: B 864 LEU cc_start: 0.9367 (tp) cc_final: 0.9115 (tt) REVERT: B 1050 MET cc_start: 0.7816 (ptt) cc_final: 0.7496 (ptt) REVERT: D 82 MET cc_start: 0.7477 (mpp) cc_final: 0.6432 (pmm) REVERT: D 123 MET cc_start: 0.1089 (tpt) cc_final: 0.0201 (ttp) REVERT: D 323 MET cc_start: 0.4161 (tpt) cc_final: 0.3861 (tpp) REVERT: D 332 MET cc_start: 0.6036 (ppp) cc_final: 0.5630 (pmm) REVERT: D 383 MET cc_start: 0.7949 (mpp) cc_final: 0.7740 (mpp) REVERT: D 462 MET cc_start: 0.6542 (mmt) cc_final: 0.5910 (ppp) REVERT: D 474 MET cc_start: 0.1147 (mmm) cc_final: 0.0282 (mmm) REVERT: D 476 LYS cc_start: 0.3380 (tttp) cc_final: 0.3166 (mtpp) outliers start: 28 outliers final: 14 residues processed: 169 average time/residue: 0.1915 time to fit residues: 57.1266 Evaluate side-chains 142 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain D residue 60 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 10 optimal weight: 10.0000 chunk 306 optimal weight: 40.0000 chunk 270 optimal weight: 2.9990 chunk 205 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 280 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.118563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077734 restraints weight = 174070.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.077300 restraints weight = 89745.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077250 restraints weight = 65205.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.077139 restraints weight = 49384.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.076939 restraints weight = 42586.014| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 35299 Z= 0.285 Angle : 0.689 15.279 48132 Z= 0.347 Chirality : 0.046 0.315 5492 Planarity : 0.004 0.056 6122 Dihedral : 5.946 58.894 5731 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.75 % Allowed : 12.89 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.12), residues: 4206 helix: 0.07 (0.14), residues: 1304 sheet: -0.91 (0.20), residues: 602 loop : -1.16 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.020 0.002 TYR A1067 PHE 0.023 0.002 PHE B 140 TRP 0.012 0.001 TRP E 168 HIS 0.007 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00616 (35198) covalent geometry : angle 0.66878 (47874) SS BOND : bond 0.00867 ( 45) SS BOND : angle 1.49637 ( 90) hydrogen bonds : bond 0.04346 ( 1143) hydrogen bonds : angle 5.54425 ( 3213) link_BETA1-4 : bond 0.00473 ( 4) link_BETA1-4 : angle 1.71495 ( 12) link_NAG-ASN : bond 0.00502 ( 52) link_NAG-ASN : angle 2.80733 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 132 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 515 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8939 (t80) REVERT: A 81 ASN cc_start: 0.8177 (p0) cc_final: 0.7810 (p0) REVERT: A 153 MET cc_start: 0.3804 (ptt) cc_final: 0.3495 (pmm) REVERT: A 779 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8503 (tm-30) REVERT: E 62 MET cc_start: 0.2155 (mmm) cc_final: 0.1264 (mmm) REVERT: E 111 ASP cc_start: 0.7908 (t0) cc_final: 0.7622 (p0) REVERT: E 141 CYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6629 (m) REVERT: E 332 MET cc_start: 0.2516 (ptt) cc_final: 0.2230 (ptt) REVERT: E 579 MET cc_start: -0.2678 (mmt) cc_final: -0.6951 (ptm) REVERT: B 100 ILE cc_start: 0.9189 (mp) cc_final: 0.8667 (tt) REVERT: B 309 GLU cc_start: 0.8684 (tp30) cc_final: 0.8441 (tm-30) REVERT: D 60 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: D 82 MET cc_start: 0.7610 (mpp) cc_final: 0.7093 (pmm) REVERT: D 323 MET cc_start: 0.4482 (tpt) cc_final: 0.3962 (tpp) REVERT: D 332 MET cc_start: 0.6182 (ppp) cc_final: 0.5768 (pmm) REVERT: D 383 MET cc_start: 0.7637 (mpp) cc_final: 0.7352 (mpp) REVERT: D 462 MET cc_start: 0.6429 (mmt) cc_final: 0.5793 (ppp) REVERT: D 474 MET cc_start: 0.0790 (mmm) cc_final: 0.0184 (mmm) REVERT: D 579 MET cc_start: 0.3559 (OUTLIER) cc_final: 0.3092 (tpt) outliers start: 65 outliers final: 35 residues processed: 187 average time/residue: 0.1822 time to fit residues: 61.0528 Evaluate side-chains 153 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 175 optimal weight: 0.6980 chunk 404 optimal weight: 40.0000 chunk 216 optimal weight: 40.0000 chunk 179 optimal weight: 0.5980 chunk 312 optimal weight: 6.9990 chunk 402 optimal weight: 50.0000 chunk 190 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 260 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 408 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 60 GLN B 437 ASN B 580 GLN B 762 GLN B 764 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.122313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.082401 restraints weight = 172459.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.082334 restraints weight = 93820.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.081969 restraints weight = 58026.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.081833 restraints weight = 43531.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081737 restraints weight = 37815.506| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35299 Z= 0.111 Angle : 0.550 15.351 48132 Z= 0.272 Chirality : 0.044 0.316 5492 Planarity : 0.003 0.055 6122 Dihedral : 5.467 58.909 5731 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.40 % Allowed : 14.16 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 4206 helix: 0.42 (0.15), residues: 1293 sheet: -0.64 (0.21), residues: 577 loop : -1.09 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.016 0.001 TYR A1067 PHE 0.022 0.001 PHE D 504 TRP 0.011 0.001 TRP E 168 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00237 (35198) covalent geometry : angle 0.53046 (47874) SS BOND : bond 0.00268 ( 45) SS BOND : angle 1.00927 ( 90) hydrogen bonds : bond 0.03777 ( 1143) hydrogen bonds : angle 5.12667 ( 3213) link_BETA1-4 : bond 0.00367 ( 4) link_BETA1-4 : angle 1.08205 ( 12) link_NAG-ASN : bond 0.00436 ( 52) link_NAG-ASN : angle 2.49714 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 858 LEU cc_start: 0.9504 (mm) cc_final: 0.9198 (pt) REVERT: A 153 MET cc_start: 0.4034 (ptt) cc_final: 0.3671 (pmm) REVERT: A 779 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 1019 ARG cc_start: 0.8741 (tpt170) cc_final: 0.8353 (tpt170) REVERT: E 62 MET cc_start: 0.1188 (mmm) cc_final: 0.0950 (mmm) REVERT: E 111 ASP cc_start: 0.7900 (t0) cc_final: 0.7613 (p0) REVERT: E 141 CYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6416 (m) REVERT: E 332 MET cc_start: 0.1482 (ptt) cc_final: 0.1216 (ptt) REVERT: E 579 MET cc_start: -0.3894 (mmt) cc_final: -0.7383 (ptm) REVERT: B 1050 MET cc_start: 0.8108 (ptt) cc_final: 0.7717 (ptt) REVERT: D 323 MET cc_start: 0.4166 (tpt) cc_final: 0.3756 (tpp) REVERT: D 332 MET cc_start: 0.5756 (ppp) cc_final: 0.5282 (pmm) REVERT: D 383 MET cc_start: 0.7660 (mpp) cc_final: 0.7260 (mpp) REVERT: D 462 MET cc_start: 0.6362 (mmt) cc_final: 0.5792 (ppp) REVERT: D 474 MET cc_start: 0.0066 (mmm) cc_final: -0.0433 (mmm) outliers start: 52 outliers final: 28 residues processed: 179 average time/residue: 0.1880 time to fit residues: 59.6416 Evaluate side-chains 154 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 434 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 17 optimal weight: 3.9990 chunk 349 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 354 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 260 optimal weight: 20.0000 chunk 153 optimal weight: 0.2980 chunk 167 optimal weight: 3.9990 chunk 328 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.122140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.081335 restraints weight = 171795.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080531 restraints weight = 82011.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.079807 restraints weight = 52284.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.080171 restraints weight = 37637.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.080365 restraints weight = 30215.905| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35299 Z= 0.117 Angle : 0.544 14.674 48132 Z= 0.267 Chirality : 0.044 0.319 5492 Planarity : 0.003 0.054 6122 Dihedral : 5.249 58.756 5731 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.43 % Allowed : 14.62 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4206 helix: 0.48 (0.15), residues: 1309 sheet: -0.60 (0.20), residues: 621 loop : -1.03 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.017 0.001 TYR A1067 PHE 0.019 0.001 PHE C 92 TRP 0.010 0.001 TRP E 168 HIS 0.010 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00258 (35198) covalent geometry : angle 0.52522 (47874) SS BOND : bond 0.00234 ( 45) SS BOND : angle 0.88962 ( 90) hydrogen bonds : bond 0.03587 ( 1143) hydrogen bonds : angle 4.94438 ( 3213) link_BETA1-4 : bond 0.00140 ( 4) link_BETA1-4 : angle 1.12107 ( 12) link_NAG-ASN : bond 0.00390 ( 52) link_NAG-ASN : angle 2.49055 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 858 LEU cc_start: 0.9477 (mm) cc_final: 0.9186 (pt) REVERT: A 779 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 1019 ARG cc_start: 0.8648 (tpt170) cc_final: 0.8277 (tpt170) REVERT: E 62 MET cc_start: 0.1713 (mmm) cc_final: 0.1448 (mmm) REVERT: E 111 ASP cc_start: 0.7840 (t0) cc_final: 0.7597 (p0) REVERT: E 141 CYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6552 (m) REVERT: E 332 MET cc_start: 0.2881 (ptt) cc_final: 0.2671 (ptt) REVERT: E 579 MET cc_start: -0.1888 (mmt) cc_final: -0.6542 (ptm) REVERT: B 100 ILE cc_start: 0.8965 (mp) cc_final: 0.8500 (tt) REVERT: B 1050 MET cc_start: 0.8166 (ptt) cc_final: 0.7742 (ptt) REVERT: D 82 MET cc_start: 0.7630 (mpp) cc_final: 0.6450 (pmm) REVERT: D 323 MET cc_start: 0.4579 (tpt) cc_final: 0.4090 (tpp) REVERT: D 332 MET cc_start: 0.5943 (ppp) cc_final: 0.5563 (pmm) REVERT: D 383 MET cc_start: 0.7777 (mpp) cc_final: 0.7442 (mpp) REVERT: D 462 MET cc_start: 0.6516 (mmt) cc_final: 0.5975 (ppp) REVERT: D 474 MET cc_start: 0.0843 (mmm) cc_final: 0.0123 (mmm) REVERT: D 579 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.3362 (tpt) outliers start: 53 outliers final: 33 residues processed: 177 average time/residue: 0.1839 time to fit residues: 58.5837 Evaluate side-chains 164 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 152 optimal weight: 8.9990 chunk 228 optimal weight: 30.0000 chunk 117 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 119 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 403 optimal weight: 50.0000 chunk 132 optimal weight: 0.0980 chunk 281 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.118447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.076904 restraints weight = 157871.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.077272 restraints weight = 81130.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.077758 restraints weight = 47529.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.076885 restraints weight = 38902.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.076978 restraints weight = 33724.695| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35299 Z= 0.197 Angle : 0.603 13.034 48132 Z= 0.301 Chirality : 0.044 0.316 5492 Planarity : 0.004 0.056 6122 Dihedral : 5.492 59.980 5731 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.83 % Allowed : 14.76 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4206 helix: 0.46 (0.15), residues: 1335 sheet: -0.76 (0.20), residues: 637 loop : -1.09 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.017 0.001 TYR A1067 PHE 0.021 0.002 PHE C 238 TRP 0.010 0.001 TRP E 168 HIS 0.009 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00432 (35198) covalent geometry : angle 0.58449 (47874) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.15252 ( 90) hydrogen bonds : bond 0.03671 ( 1143) hydrogen bonds : angle 5.05520 ( 3213) link_BETA1-4 : bond 0.00438 ( 4) link_BETA1-4 : angle 1.19341 ( 12) link_NAG-ASN : bond 0.00429 ( 52) link_NAG-ASN : angle 2.52522 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 125 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 275 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: C 858 LEU cc_start: 0.9423 (mm) cc_final: 0.9165 (pp) REVERT: C 895 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8338 (pp30) REVERT: A 779 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8525 (tm-30) REVERT: E 62 MET cc_start: 0.1745 (mmm) cc_final: 0.1491 (mmm) REVERT: E 111 ASP cc_start: 0.7893 (t0) cc_final: 0.7612 (p0) REVERT: E 141 CYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6116 (m) REVERT: E 297 MET cc_start: 0.0699 (mmt) cc_final: -0.0142 (mpp) REVERT: E 323 MET cc_start: 0.5443 (tpp) cc_final: 0.4844 (tpp) REVERT: E 455 MET cc_start: 0.2986 (ppp) cc_final: 0.1779 (mpp) REVERT: E 579 MET cc_start: -0.2554 (mmt) cc_final: -0.6916 (ptm) REVERT: B 153 MET cc_start: 0.4546 (pmm) cc_final: 0.4121 (mpp) REVERT: B 1050 MET cc_start: 0.8353 (ptt) cc_final: 0.8019 (ptt) REVERT: D 62 MET cc_start: 0.4772 (mpp) cc_final: 0.4544 (mpp) REVERT: D 82 MET cc_start: 0.7715 (mpp) cc_final: 0.6453 (pmm) REVERT: D 323 MET cc_start: 0.4672 (tpt) cc_final: 0.4163 (tpp) REVERT: D 332 MET cc_start: 0.5634 (ppp) cc_final: 0.5216 (pmm) REVERT: D 383 MET cc_start: 0.7783 (mpp) cc_final: 0.7466 (mpp) REVERT: D 462 MET cc_start: 0.6438 (mmt) cc_final: 0.5921 (ppp) REVERT: D 476 LYS cc_start: 0.3796 (tttp) cc_final: 0.3588 (mtpp) REVERT: D 579 MET cc_start: 0.3075 (OUTLIER) cc_final: 0.2730 (tpt) outliers start: 68 outliers final: 47 residues processed: 184 average time/residue: 0.1776 time to fit residues: 59.0587 Evaluate side-chains 167 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 385 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 414 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 343 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN E 373 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.118591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.078326 restraints weight = 155241.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077860 restraints weight = 85967.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.077739 restraints weight = 49698.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.077385 restraints weight = 39452.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.077382 restraints weight = 35127.270| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35299 Z= 0.175 Angle : 0.578 12.757 48132 Z= 0.286 Chirality : 0.044 0.316 5492 Planarity : 0.004 0.056 6122 Dihedral : 5.438 59.662 5731 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.59 % Allowed : 15.24 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4206 helix: 0.56 (0.15), residues: 1328 sheet: -0.72 (0.20), residues: 623 loop : -1.09 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.018 0.001 TYR A1067 PHE 0.021 0.001 PHE C 238 TRP 0.009 0.001 TRP E 168 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00384 (35198) covalent geometry : angle 0.55988 (47874) SS BOND : bond 0.00476 ( 45) SS BOND : angle 1.07692 ( 90) hydrogen bonds : bond 0.03550 ( 1143) hydrogen bonds : angle 4.95459 ( 3213) link_BETA1-4 : bond 0.00217 ( 4) link_BETA1-4 : angle 1.08534 ( 12) link_NAG-ASN : bond 0.00372 ( 52) link_NAG-ASN : angle 2.47445 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 275 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: C 755 GLN cc_start: 0.9075 (pt0) cc_final: 0.8863 (tt0) REVERT: C 858 LEU cc_start: 0.9473 (mm) cc_final: 0.9188 (pp) REVERT: A 779 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8519 (tm-30) REVERT: E 62 MET cc_start: 0.2108 (mmm) cc_final: 0.1837 (mmm) REVERT: E 111 ASP cc_start: 0.7893 (t0) cc_final: 0.7633 (p0) REVERT: E 141 CYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6214 (m) REVERT: E 323 MET cc_start: 0.6555 (tpp) cc_final: 0.5975 (tpp) REVERT: E 455 MET cc_start: 0.2535 (ppp) cc_final: 0.1196 (mpp) REVERT: E 579 MET cc_start: -0.1047 (mmt) cc_final: -0.6023 (ptm) REVERT: B 153 MET cc_start: 0.4224 (pmm) cc_final: 0.3847 (mpp) REVERT: D 62 MET cc_start: 0.5006 (mpp) cc_final: 0.4759 (mpp) REVERT: D 82 MET cc_start: 0.7699 (mpp) cc_final: 0.6494 (pmm) REVERT: D 132 VAL cc_start: -0.2251 (OUTLIER) cc_final: -0.2764 (p) REVERT: D 270 MET cc_start: -0.1496 (mtt) cc_final: -0.2258 (tpp) REVERT: D 323 MET cc_start: 0.4969 (tpt) cc_final: 0.4426 (tpp) REVERT: D 332 MET cc_start: 0.5912 (ppp) cc_final: 0.5544 (pmm) REVERT: D 383 MET cc_start: 0.7751 (mpp) cc_final: 0.7452 (mpp) REVERT: D 462 MET cc_start: 0.6537 (mmt) cc_final: 0.6030 (ppp) REVERT: D 474 MET cc_start: 0.1026 (mmm) cc_final: -0.0055 (mmm) REVERT: D 476 LYS cc_start: 0.3909 (tttp) cc_final: 0.3707 (mtpp) REVERT: D 579 MET cc_start: 0.3980 (OUTLIER) cc_final: 0.3629 (tpt) outliers start: 59 outliers final: 44 residues processed: 168 average time/residue: 0.1698 time to fit residues: 51.4554 Evaluate side-chains 165 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 313 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 385 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 185 optimal weight: 0.1980 chunk 423 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 353 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.119395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079500 restraints weight = 153644.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.079251 restraints weight = 85192.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.078846 restraints weight = 49475.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.078977 restraints weight = 38552.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.079233 restraints weight = 35062.063| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35299 Z= 0.119 Angle : 0.552 12.597 48132 Z= 0.272 Chirality : 0.044 0.315 5492 Planarity : 0.003 0.057 6122 Dihedral : 5.265 59.201 5731 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.35 % Allowed : 15.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4206 helix: 0.67 (0.15), residues: 1318 sheet: -0.60 (0.20), residues: 615 loop : -1.04 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.016 0.001 TYR A1067 PHE 0.022 0.001 PHE C 515 TRP 0.010 0.001 TRP E 168 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00264 (35198) covalent geometry : angle 0.53425 (47874) SS BOND : bond 0.00288 ( 45) SS BOND : angle 0.94549 ( 90) hydrogen bonds : bond 0.03383 ( 1143) hydrogen bonds : angle 4.82653 ( 3213) link_BETA1-4 : bond 0.00142 ( 4) link_BETA1-4 : angle 0.98677 ( 12) link_NAG-ASN : bond 0.00418 ( 52) link_NAG-ASN : angle 2.39726 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 515 PHE cc_start: 0.9104 (t80) cc_final: 0.8747 (t80) REVERT: C 755 GLN cc_start: 0.9070 (pt0) cc_final: 0.8858 (tt0) REVERT: C 773 GLU cc_start: 0.8704 (pp20) cc_final: 0.8384 (pp20) REVERT: C 858 LEU cc_start: 0.9480 (mm) cc_final: 0.9215 (pp) REVERT: A 779 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 904 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: A 1019 ARG cc_start: 0.8697 (tpt170) cc_final: 0.8258 (tpt170) REVERT: E 62 MET cc_start: 0.1484 (mmm) cc_final: 0.1263 (mmm) REVERT: E 111 ASP cc_start: 0.7890 (t0) cc_final: 0.7575 (p0) REVERT: E 297 MET cc_start: 0.0280 (mmt) cc_final: -0.0676 (mpp) REVERT: E 323 MET cc_start: 0.4483 (tpp) cc_final: 0.3888 (tpp) REVERT: E 455 MET cc_start: 0.3146 (ppp) cc_final: 0.1648 (mpp) REVERT: E 579 MET cc_start: -0.3702 (mmt) cc_final: -0.7282 (ptm) REVERT: B 153 MET cc_start: 0.4244 (pmm) cc_final: 0.3876 (mpp) REVERT: B 697 MET cc_start: 0.9026 (tpp) cc_final: 0.8680 (tpp) REVERT: B 869 MET cc_start: 0.8774 (ptt) cc_final: 0.8449 (pmm) REVERT: D 62 MET cc_start: 0.4348 (mpp) cc_final: 0.4057 (mpp) REVERT: D 82 MET cc_start: 0.7742 (mpp) cc_final: 0.6374 (pmm) REVERT: D 270 MET cc_start: -0.1402 (mtt) cc_final: -0.2055 (tpp) REVERT: D 323 MET cc_start: 0.4611 (tpt) cc_final: 0.4206 (tpp) REVERT: D 332 MET cc_start: 0.5412 (ppp) cc_final: 0.4937 (pmm) REVERT: D 383 MET cc_start: 0.7692 (mpp) cc_final: 0.7307 (mpp) REVERT: D 462 MET cc_start: 0.6355 (mmt) cc_final: 0.5882 (ppp) REVERT: D 474 MET cc_start: 0.0057 (mmm) cc_final: -0.0894 (mmm) REVERT: D 579 MET cc_start: 0.2367 (OUTLIER) cc_final: 0.2048 (tpt) outliers start: 50 outliers final: 41 residues processed: 163 average time/residue: 0.1854 time to fit residues: 54.0129 Evaluate side-chains 163 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 288 optimal weight: 0.8980 chunk 405 optimal weight: 8.9990 chunk 385 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 381 optimal weight: 5.9990 chunk 355 optimal weight: 0.0370 chunk 168 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 268 optimal weight: 0.0870 chunk 275 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.118818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.078598 restraints weight = 153236.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.078374 restraints weight = 78854.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.077755 restraints weight = 48644.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.077465 restraints weight = 37835.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.077632 restraints weight = 35184.256| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35299 Z= 0.147 Angle : 0.565 11.961 48132 Z= 0.279 Chirality : 0.044 0.313 5492 Planarity : 0.004 0.057 6122 Dihedral : 5.255 59.297 5731 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.43 % Allowed : 15.83 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4206 helix: 0.70 (0.15), residues: 1321 sheet: -0.66 (0.20), residues: 622 loop : -1.02 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.017 0.001 TYR A1067 PHE 0.036 0.001 PHE C 392 TRP 0.009 0.001 TRP E 168 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00325 (35198) covalent geometry : angle 0.54779 (47874) SS BOND : bond 0.00336 ( 45) SS BOND : angle 0.98691 ( 90) hydrogen bonds : bond 0.03373 ( 1143) hydrogen bonds : angle 4.80631 ( 3213) link_BETA1-4 : bond 0.00179 ( 4) link_BETA1-4 : angle 1.06929 ( 12) link_NAG-ASN : bond 0.00365 ( 52) link_NAG-ASN : angle 2.40408 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 275 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: C 392 PHE cc_start: 0.5552 (t80) cc_final: 0.5188 (t80) REVERT: C 515 PHE cc_start: 0.9113 (t80) cc_final: 0.8873 (t80) REVERT: C 755 GLN cc_start: 0.9065 (pt0) cc_final: 0.8825 (tt0) REVERT: C 773 GLU cc_start: 0.8720 (pp20) cc_final: 0.8415 (pp20) REVERT: C 858 LEU cc_start: 0.9480 (mm) cc_final: 0.9208 (pp) REVERT: A 779 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 904 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: A 1019 ARG cc_start: 0.8696 (tpt170) cc_final: 0.8266 (tpt170) REVERT: E 62 MET cc_start: 0.1895 (mmm) cc_final: 0.1619 (mmm) REVERT: E 111 ASP cc_start: 0.7887 (t0) cc_final: 0.7614 (p0) REVERT: E 297 MET cc_start: 0.1060 (mmt) cc_final: 0.0257 (mpp) REVERT: E 323 MET cc_start: 0.6183 (tpp) cc_final: 0.5533 (tpp) REVERT: E 455 MET cc_start: 0.2677 (ppp) cc_final: 0.1105 (mpp) REVERT: E 579 MET cc_start: -0.1953 (mmt) cc_final: -0.6502 (ptm) REVERT: B 130 VAL cc_start: 0.5605 (OUTLIER) cc_final: 0.5390 (t) REVERT: B 153 MET cc_start: 0.3727 (pmm) cc_final: 0.3268 (mpp) REVERT: B 697 MET cc_start: 0.9065 (tpp) cc_final: 0.8729 (tpp) REVERT: B 869 MET cc_start: 0.8779 (ptt) cc_final: 0.8445 (pmm) REVERT: D 62 MET cc_start: 0.4855 (mpp) cc_final: 0.4577 (mpp) REVERT: D 82 MET cc_start: 0.7746 (mpp) cc_final: 0.6517 (pmm) REVERT: D 132 VAL cc_start: -0.2457 (OUTLIER) cc_final: -0.2932 (p) REVERT: D 270 MET cc_start: -0.1437 (mtt) cc_final: -0.2072 (tpp) REVERT: D 323 MET cc_start: 0.5060 (tpt) cc_final: 0.4518 (tpp) REVERT: D 332 MET cc_start: 0.5989 (ppp) cc_final: 0.5597 (pmm) REVERT: D 383 MET cc_start: 0.7743 (mpp) cc_final: 0.7415 (mpp) REVERT: D 462 MET cc_start: 0.6451 (mmt) cc_final: 0.5966 (ppp) REVERT: D 474 MET cc_start: 0.0322 (mmm) cc_final: -0.0517 (mmm) REVERT: D 579 MET cc_start: 0.3485 (OUTLIER) cc_final: 0.3008 (tpt) outliers start: 53 outliers final: 46 residues processed: 166 average time/residue: 0.1729 time to fit residues: 51.4448 Evaluate side-chains 171 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 24 optimal weight: 2.9990 chunk 342 optimal weight: 0.0770 chunk 301 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 271 optimal weight: 20.0000 chunk 278 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.122225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.080649 restraints weight = 153443.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.080440 restraints weight = 79727.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.081629 restraints weight = 43849.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.080591 restraints weight = 30374.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.080639 restraints weight = 28943.282| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35299 Z= 0.100 Angle : 0.549 11.932 48132 Z= 0.270 Chirality : 0.044 0.315 5492 Planarity : 0.003 0.058 6122 Dihedral : 5.086 58.679 5731 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.32 % Allowed : 15.89 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 4206 helix: 0.76 (0.15), residues: 1319 sheet: -0.49 (0.21), residues: 617 loop : -0.97 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1019 TYR 0.024 0.001 TYR C 489 PHE 0.029 0.001 PHE C 392 TRP 0.010 0.001 TRP E 168 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00222 (35198) covalent geometry : angle 0.53308 (47874) SS BOND : bond 0.00254 ( 45) SS BOND : angle 0.83580 ( 90) hydrogen bonds : bond 0.03235 ( 1143) hydrogen bonds : angle 4.68606 ( 3213) link_BETA1-4 : bond 0.00193 ( 4) link_BETA1-4 : angle 0.95493 ( 12) link_NAG-ASN : bond 0.00390 ( 52) link_NAG-ASN : angle 2.27431 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8539.01 seconds wall clock time: 147 minutes 14.03 seconds (8834.03 seconds total)