Starting phenix.real_space_refine on Fri Mar 6 10:49:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydy_33760/03_2026/7ydy_33760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydy_33760/03_2026/7ydy_33760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ydy_33760/03_2026/7ydy_33760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydy_33760/03_2026/7ydy_33760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ydy_33760/03_2026/7ydy_33760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydy_33760/03_2026/7ydy_33760.map" } resolution = 4.75 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1499 atoms to isotropic. 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 127 5.16 5 C 18280 2.51 5 N 4756 2.21 5 O 5597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 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: 28760 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.90, per 1000 atoms: 0.24 Number of scatterers: 28760 At special positions: 0 Unit cell: (179.52, 161.92, 197.12, 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 127 16.00 O 5597 8.00 N 4756 7.00 C 18280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 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 C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.04 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6788 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 65 sheets defined 16.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.618A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.110A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.804A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 748 through 754 removed outlier: 3.881A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.663A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.241A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.042A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.503A pdb=" N GLU A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.955A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.652A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.555A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.554A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 949 through 966 removed outlier: 3.888A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.075A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1032 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.667A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.744A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.924A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.695A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (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 908 removed outlier: 3.719A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 946 through 966 removed outlier: 4.178A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.892A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1030 Processing helix chain 'H' and resid 196 through 200 removed outlier: 3.543A pdb=" N SER H 199 " --> pdb=" O PRO H 196 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 200' Processing helix chain 'L' and resid 129 through 133 removed outlier: 3.704A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.069A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.785A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.683A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.480A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.319A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.044A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.537A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.525A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.706A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.545A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.666A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.557A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.408A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 3.697A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.589A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.602A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.507A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.458A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.177A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.626A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.791A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.698A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.531A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 160 removed outlier: 5.302A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.997A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 597 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.581A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 355 through 358 removed outlier: 6.266A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.531A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.726A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.545A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.436A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.669A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.507A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.755A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.755A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 735 removed outlier: 4.194A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.665A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.801A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.583A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.765A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.983A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.694A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 355 through 358 removed outlier: 5.604A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.668A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.381A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.510A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.753A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 724 through 727 removed outlier: 3.504A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.527A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.648A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.167A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.845A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.845A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.526A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 163 through 165 removed outlier: 4.191A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 209 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 218 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 216 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 17 through 23 removed outlier: 4.202A pdb=" N CYS L 22 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA L 73 " --> pdb=" O CYS L 22 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.833A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER L 92 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL L 101 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.833A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR L 106 " --> pdb=" O TYR L 88 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.121A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AH1, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.767A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 197 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.767A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 197 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL L 211 " --> pdb=" O TYR L 196 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2183 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: 7.11 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9215 1.34 - 1.46: 7154 1.46 - 1.58: 12897 1.58 - 1.70: 0 1.70 - 1.82: 159 Bond restraints: 29425 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C3 NAG B1301 " pdb=" O3 NAG B1301 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 29420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 39171 1.40 - 2.80: 776 2.80 - 4.20: 92 4.20 - 5.60: 17 5.60 - 7.00: 7 Bond angle restraints: 40063 Sorted by residual: angle pdb=" C ILE C 896 " pdb=" N PRO C 897 " pdb=" CA PRO C 897 " ideal model delta sigma weight residual 120.03 116.11 3.92 9.90e-01 1.02e+00 1.57e+01 angle pdb=" N VAL B 524 " pdb=" CA VAL B 524 " pdb=" C VAL B 524 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" CA GLY B 431 " pdb=" C GLY B 431 " pdb=" O GLY B 431 " ideal model delta sigma weight residual 122.45 119.94 2.51 7.20e-01 1.93e+00 1.21e+01 angle pdb=" CA GLY C 431 " pdb=" C GLY C 431 " pdb=" O GLY C 431 " ideal model delta sigma weight residual 122.52 119.95 2.57 7.90e-01 1.60e+00 1.06e+01 angle pdb=" CA PHE B 898 " pdb=" C PHE B 898 " pdb=" N PRO B 899 " ideal model delta sigma weight residual 120.79 117.77 3.02 9.70e-01 1.06e+00 9.71e+00 ... (remaining 40058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 17016 17.63 - 35.26: 833 35.26 - 52.89: 141 52.89 - 70.52: 38 70.52 - 88.16: 9 Dihedral angle restraints: 18037 sinusoidal: 7466 harmonic: 10571 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.97 82.03 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 17.99 75.01 1 1.00e+01 1.00e-02 7.12e+01 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 93.00 27.08 65.92 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 18034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3944 0.055 - 0.111: 632 0.111 - 0.166: 54 0.166 - 0.222: 3 0.222 - 0.277: 3 Chirality restraints: 4636 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4633 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG B1301 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG A1301 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " -0.014 2.00e-02 2.50e+03 1.63e-02 3.31e+00 pdb=" CG ASN A 282 " 0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.020 2.00e-02 2.50e+03 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6355 2.78 - 3.31: 24677 3.31 - 3.84: 45813 3.84 - 4.37: 51009 4.37 - 4.90: 90536 Nonbonded interactions: 218390 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.253 3.040 nonbonded pdb=" OG SER L 21 " pdb=" O ALA L 73 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.308 3.040 ... (remaining 218385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.540 Find NCS groups from input model: 0.530 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5402 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 : 0.002 0.038 29508 Z= 0.124 Angle : 0.465 8.599 40265 Z= 0.251 Chirality : 0.042 0.277 4636 Planarity : 0.003 0.036 5150 Dihedral : 10.394 88.155 11108 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 0.44 % Allowed : 2.02 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -3.89 (0.11), residues: 3600 helix: -2.22 (0.14), residues: 570 sheet: -1.64 (0.18), residues: 677 loop : -3.18 (0.10), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.006 0.000 TYR A 495 PHE 0.010 0.000 PHE B 486 TRP 0.002 0.000 TRP A 436 HIS 0.001 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00233 (29425) covalent geometry : angle 0.45394 (40063) SS BOND : bond 0.00166 ( 47) SS BOND : angle 0.57964 ( 94) hydrogen bonds : bond 0.26190 ( 783) hydrogen bonds : angle 9.03761 ( 2183) link_BETA1-4 : bond 0.00275 ( 6) link_BETA1-4 : angle 0.81917 ( 18) link_NAG-ASN : bond 0.00527 ( 30) link_NAG-ASN : angle 2.15686 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 573 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.8435 (t80) cc_final: 0.8193 (t80) REVERT: A 117 LEU cc_start: 0.8102 (tt) cc_final: 0.7824 (mt) REVERT: A 157 PHE cc_start: 0.6348 (t80) cc_final: 0.6023 (t80) REVERT: A 177 MET cc_start: -0.0082 (mmt) cc_final: -0.3518 (ttt) REVERT: A 238 PHE cc_start: 0.5773 (p90) cc_final: 0.5560 (p90) REVERT: A 242 LEU cc_start: 0.7813 (tp) cc_final: 0.7402 (tp) REVERT: A 244 LEU cc_start: 0.4697 (pt) cc_final: 0.4204 (mp) REVERT: A 321 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8349 (mp10) REVERT: A 697 MET cc_start: 0.6710 (ptm) cc_final: 0.6308 (mpp) REVERT: A 736 VAL cc_start: 0.8852 (t) cc_final: 0.8600 (m) REVERT: A 742 ILE cc_start: 0.7839 (mt) cc_final: 0.7490 (mp) REVERT: A 773 GLU cc_start: 0.8173 (tt0) cc_final: 0.7712 (mt-10) REVERT: A 859 THR cc_start: 0.7032 (p) cc_final: 0.6164 (p) REVERT: A 867 ASP cc_start: 0.9076 (m-30) cc_final: 0.8768 (t0) REVERT: A 878 LEU cc_start: 0.8080 (mt) cc_final: 0.7819 (mt) REVERT: A 896 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4950 (tp) REVERT: A 1018 ILE cc_start: 0.7449 (mm) cc_final: 0.7140 (mm) REVERT: A 1033 VAL cc_start: 0.6904 (t) cc_final: 0.6112 (t) REVERT: A 1118 ASP cc_start: 0.8625 (m-30) cc_final: 0.8355 (p0) REVERT: B 133 PHE cc_start: 0.6725 (m-80) cc_final: 0.6368 (m-80) REVERT: B 153 MET cc_start: 0.7346 (mmm) cc_final: 0.7115 (ppp) REVERT: B 177 MET cc_start: -0.1667 (mmt) cc_final: -0.3613 (ttt) REVERT: B 235 ILE cc_start: 0.5145 (mt) cc_final: 0.3805 (mm) REVERT: B 297 SER cc_start: 0.7358 (p) cc_final: 0.7093 (t) REVERT: B 380 TYR cc_start: 0.7581 (m-80) cc_final: 0.7224 (m-80) REVERT: B 421 TYR cc_start: 0.8495 (m-80) cc_final: 0.7909 (m-10) REVERT: B 578 ASP cc_start: 0.8326 (t0) cc_final: 0.7891 (m-30) REVERT: B 599 THR cc_start: 0.6959 (t) cc_final: 0.5952 (p) REVERT: B 697 MET cc_start: 0.7282 (ptm) cc_final: 0.7077 (tpt) REVERT: B 702 GLU cc_start: 0.7631 (tp30) cc_final: 0.7165 (mp0) REVERT: B 740 MET cc_start: 0.6733 (ttm) cc_final: 0.5935 (tpp) REVERT: B 762 GLN cc_start: 0.8370 (mt0) cc_final: 0.7914 (mp10) REVERT: B 788 ILE cc_start: 0.7445 (mm) cc_final: 0.7185 (mt) REVERT: B 866 THR cc_start: 0.6961 (p) cc_final: 0.6521 (t) REVERT: B 882 ILE cc_start: 0.8230 (pt) cc_final: 0.7578 (pt) REVERT: B 901 GLN cc_start: 0.6869 (tt0) cc_final: 0.6397 (tm-30) REVERT: B 921 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8431 (mmmt) REVERT: B 953 ASN cc_start: 0.6788 (m-40) cc_final: 0.6483 (m-40) REVERT: B 993 ILE cc_start: 0.8812 (mt) cc_final: 0.8448 (mm) REVERT: B 996 LEU cc_start: 0.7783 (mt) cc_final: 0.7453 (tp) REVERT: B 997 ILE cc_start: 0.8678 (mt) cc_final: 0.7940 (mm) REVERT: B 1001 LEU cc_start: 0.8438 (tp) cc_final: 0.8237 (mm) REVERT: B 1005 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7513 (mt0) REVERT: B 1018 ILE cc_start: 0.8171 (mm) cc_final: 0.7965 (pt) REVERT: B 1019 ARG cc_start: 0.7893 (tpt-90) cc_final: 0.7586 (tpt170) REVERT: B 1033 VAL cc_start: 0.3815 (t) cc_final: 0.1783 (t) REVERT: B 1077 THR cc_start: 0.6976 (t) cc_final: 0.6534 (t) REVERT: C 48 LEU cc_start: 0.7000 (mt) cc_final: 0.6473 (tp) REVERT: C 177 MET cc_start: 0.1146 (mmt) cc_final: 0.0339 (ttp) REVERT: C 321 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7668 (mm-40) REVERT: C 408 ARG cc_start: 0.7301 (ppt170) cc_final: 0.7040 (tmm-80) REVERT: C 654 GLU cc_start: 0.8275 (pt0) cc_final: 0.7736 (mp0) REVERT: C 740 MET cc_start: 0.6416 (ttm) cc_final: 0.5791 (tpt) REVERT: C 762 GLN cc_start: 0.8196 (mt0) cc_final: 0.7625 (tp40) REVERT: C 794 ILE cc_start: 0.6904 (mt) cc_final: 0.6658 (tp) REVERT: C 814 LYS cc_start: 0.8093 (tptt) cc_final: 0.7860 (mmmt) REVERT: C 882 ILE cc_start: 0.8407 (pt) cc_final: 0.7829 (pt) REVERT: C 960 ASN cc_start: 0.7496 (m-40) cc_final: 0.6580 (t0) REVERT: C 980 ILE cc_start: 0.7572 (pt) cc_final: 0.7294 (pt) REVERT: C 992 GLN cc_start: 0.6535 (mm110) cc_final: 0.6099 (tt0) REVERT: C 1008 VAL cc_start: 0.7107 (t) cc_final: 0.6638 (t) REVERT: C 1029 MET cc_start: 0.7257 (tpp) cc_final: 0.6993 (tpp) REVERT: C 1033 VAL cc_start: 0.5616 (t) cc_final: 0.3057 (t) REVERT: C 1034 LEU cc_start: 0.5029 (mt) cc_final: 0.4696 (mt) REVERT: H 105 TYR cc_start: 0.7089 (m-80) cc_final: 0.6707 (t80) REVERT: H 225 LYS cc_start: 0.3447 (mptt) cc_final: 0.2138 (mttt) REVERT: L 29 ILE cc_start: 0.6933 (tt) cc_final: 0.6595 (pt) REVERT: L 36 HIS cc_start: 0.2416 (m-70) cc_final: 0.1026 (m-70) outliers start: 13 outliers final: 1 residues processed: 583 average time/residue: 0.2100 time to fit residues: 189.9850 Evaluate side-chains 274 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.0770 chunk 298 optimal weight: 9.9990 overall best weight: 4.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 66 HIS A 149 ASN A 183 GLN A 196 ASN A 218 GLN A 271 GLN A 360 ASN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 474 GLN A 493 GLN A 580 GLN A 613 GLN A 675 GLN A 774 GLN A 926 GLN A 935 GLN A 949 GLN A 953 ASN A 992 GLN A1048 HIS ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 69 HIS B 99 ASN B 146 HIS B 183 GLN B 196 ASN B 207 HIS B 218 GLN B 271 GLN B 437 ASN B 448 ASN B 493 GLN B 498 GLN B 544 ASN B 613 GLN B 675 GLN B 762 GLN B 926 GLN B 935 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 66 HIS C 183 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN C 271 GLN C 314 GLN C 437 ASN C 448 ASN C 487 ASN C 493 GLN C 536 ASN C 542 ASN C 751 ASN C 762 GLN C 804 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 935 GLN C 957 GLN C1064 HIS H 166 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.092992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.070218 restraints weight = 230161.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.071995 restraints weight = 144888.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.072938 restraints weight = 95159.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.073991 restraints weight = 64701.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073908 restraints weight = 51774.355| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 29508 Z= 0.240 Angle : 0.732 13.290 40265 Z= 0.370 Chirality : 0.049 0.395 4636 Planarity : 0.005 0.055 5150 Dihedral : 5.248 59.891 4656 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.06 % Allowed : 6.74 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.68 (0.12), residues: 3600 helix: 0.42 (0.22), residues: 589 sheet: -1.16 (0.17), residues: 782 loop : -2.81 (0.11), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 38 TYR 0.031 0.002 TYR C 170 PHE 0.032 0.002 PHE C 906 TRP 0.041 0.003 TRP H 114 HIS 0.008 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00514 (29425) covalent geometry : angle 0.72035 (40063) SS BOND : bond 0.01833 ( 47) SS BOND : angle 1.46984 ( 94) hydrogen bonds : bond 0.04428 ( 783) hydrogen bonds : angle 6.25566 ( 2183) link_BETA1-4 : bond 0.00528 ( 6) link_BETA1-4 : angle 1.50775 ( 18) link_NAG-ASN : bond 0.00667 ( 30) link_NAG-ASN : angle 2.50608 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8641 (tt) cc_final: 0.8161 (mt) REVERT: A 157 PHE cc_start: 0.6575 (t80) cc_final: 0.6281 (t80) REVERT: A 177 MET cc_start: -0.1048 (mmt) cc_final: -0.4381 (ttt) REVERT: A 200 TYR cc_start: 0.5297 (m-80) cc_final: 0.4771 (m-10) REVERT: A 204 TYR cc_start: 0.7383 (m-80) cc_final: 0.6176 (m-80) REVERT: A 380 TYR cc_start: 0.6113 (t80) cc_final: 0.5873 (t80) REVERT: A 902 MET cc_start: 0.8556 (mmm) cc_final: 0.7832 (tpp) REVERT: A 1041 ASP cc_start: 0.7736 (t0) cc_final: 0.7475 (t0) REVERT: B 104 TRP cc_start: 0.5593 (m-90) cc_final: 0.5370 (m-90) REVERT: B 153 MET cc_start: 0.7487 (mmm) cc_final: 0.6893 (ppp) REVERT: B 177 MET cc_start: -0.3190 (mmt) cc_final: -0.4943 (ttt) REVERT: B 204 TYR cc_start: 0.7524 (m-80) cc_final: 0.6686 (m-10) REVERT: B 224 GLU cc_start: 0.8836 (pm20) cc_final: 0.8213 (pm20) REVERT: B 421 TYR cc_start: 0.8089 (m-80) cc_final: 0.6853 (m-10) REVERT: B 461 LEU cc_start: 0.4934 (mt) cc_final: 0.4389 (mt) REVERT: B 740 MET cc_start: 0.6935 (ttm) cc_final: 0.6074 (tpp) REVERT: B 762 GLN cc_start: 0.8699 (mt0) cc_final: 0.8273 (mt0) REVERT: B 898 PHE cc_start: 0.6967 (t80) cc_final: 0.5724 (t80) REVERT: B 902 MET cc_start: 0.6917 (mmt) cc_final: 0.6256 (mpp) REVERT: B 921 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8485 (mmmt) REVERT: B 1029 MET cc_start: 0.7992 (ttm) cc_final: 0.7525 (ttm) REVERT: B 1041 ASP cc_start: 0.7909 (t0) cc_final: 0.7665 (t0) REVERT: C 177 MET cc_start: -0.1422 (mmt) cc_final: -0.2072 (ttt) REVERT: C 245 HIS cc_start: 0.2581 (m-70) cc_final: 0.2238 (m-70) REVERT: C 529 LYS cc_start: 0.3039 (tttt) cc_final: 0.2823 (mttp) REVERT: C 614 ASP cc_start: 0.3301 (t0) cc_final: 0.3038 (t0) REVERT: C 740 MET cc_start: 0.5864 (ttm) cc_final: 0.5229 (tpt) REVERT: C 898 PHE cc_start: 0.7830 (t80) cc_final: 0.7392 (t80) REVERT: C 902 MET cc_start: 0.6923 (mmm) cc_final: 0.6004 (mmm) REVERT: C 960 ASN cc_start: 0.7422 (m-40) cc_final: 0.6603 (t0) REVERT: C 1005 GLN cc_start: 0.7526 (tp-100) cc_final: 0.7214 (mm-40) REVERT: C 1029 MET cc_start: 0.7425 (tpp) cc_final: 0.6823 (tpp) REVERT: C 1031 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5683 (mt-10) REVERT: C 1041 ASP cc_start: 0.7131 (t0) cc_final: 0.6848 (t70) REVERT: H 81 MET cc_start: 0.4851 (tmm) cc_final: 0.3672 (tpp) REVERT: H 105 TYR cc_start: 0.6878 (m-80) cc_final: 0.6224 (t80) REVERT: H 220 LYS cc_start: 0.4404 (tttp) cc_final: 0.4058 (ptmm) REVERT: H 225 LYS cc_start: 0.0616 (mptt) cc_final: -0.0996 (mttt) REVERT: L 60 VAL cc_start: -0.0186 (p) cc_final: -0.0391 (t) outliers start: 2 outliers final: 1 residues processed: 310 average time/residue: 0.1873 time to fit residues: 93.5201 Evaluate side-chains 175 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 301 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 304 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 324 optimal weight: 0.8980 chunk 232 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A1002 GLN A1064 HIS A1125 ASN B 146 HIS B 563 GLN B 901 GLN B1048 HIS C 146 HIS C 196 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS L 189 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.091589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.068613 restraints weight = 227251.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.070459 restraints weight = 142958.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.071536 restraints weight = 89361.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.072054 restraints weight = 61348.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.072324 restraints weight = 52596.883| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29508 Z= 0.142 Angle : 0.565 9.269 40265 Z= 0.284 Chirality : 0.045 0.373 4636 Planarity : 0.004 0.075 5150 Dihedral : 4.588 56.166 4656 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.16 (0.13), residues: 3600 helix: 1.42 (0.23), residues: 566 sheet: -0.95 (0.17), residues: 808 loop : -2.55 (0.11), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 214 TYR 0.027 0.001 TYR L 145 PHE 0.033 0.002 PHE C 823 TRP 0.022 0.002 TRP H 114 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00315 (29425) covalent geometry : angle 0.55269 (40063) SS BOND : bond 0.00614 ( 47) SS BOND : angle 1.22194 ( 94) hydrogen bonds : bond 0.03847 ( 783) hydrogen bonds : angle 5.61860 ( 2183) link_BETA1-4 : bond 0.00447 ( 6) link_BETA1-4 : angle 1.09325 ( 18) link_NAG-ASN : bond 0.00492 ( 30) link_NAG-ASN : angle 2.20753 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8905 (tt) cc_final: 0.8524 (mt) REVERT: A 177 MET cc_start: -0.0939 (mmt) cc_final: -0.4024 (tmm) REVERT: A 204 TYR cc_start: 0.7721 (m-80) cc_final: 0.6314 (m-10) REVERT: A 697 MET cc_start: 0.7973 (tpt) cc_final: 0.7772 (tpt) REVERT: A 1041 ASP cc_start: 0.7783 (t0) cc_final: 0.7535 (t0) REVERT: A 1050 MET cc_start: 0.8148 (pmm) cc_final: 0.7180 (pmm) REVERT: B 153 MET cc_start: 0.7263 (mmm) cc_final: 0.6600 (ppp) REVERT: B 177 MET cc_start: -0.1484 (mmt) cc_final: -0.3608 (ttt) REVERT: B 204 TYR cc_start: 0.7233 (m-80) cc_final: 0.6965 (m-80) REVERT: B 224 GLU cc_start: 0.8896 (pm20) cc_final: 0.8296 (pm20) REVERT: B 421 TYR cc_start: 0.8179 (m-80) cc_final: 0.7007 (m-10) REVERT: B 434 ILE cc_start: 0.8361 (mm) cc_final: 0.8120 (mm) REVERT: B 740 MET cc_start: 0.6847 (ttm) cc_final: 0.6252 (tpp) REVERT: B 898 PHE cc_start: 0.7244 (t80) cc_final: 0.6387 (t80) REVERT: B 900 MET cc_start: 0.8033 (mtp) cc_final: 0.7825 (mtm) REVERT: B 909 ILE cc_start: 0.5908 (pt) cc_final: 0.5122 (mt) REVERT: B 911 VAL cc_start: 0.7855 (t) cc_final: 0.7611 (t) REVERT: B 921 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8428 (mmmt) REVERT: B 1018 ILE cc_start: 0.9221 (mm) cc_final: 0.8854 (mm) REVERT: B 1029 MET cc_start: 0.7924 (ttm) cc_final: 0.7420 (ttm) REVERT: C 141 LEU cc_start: 0.7987 (mp) cc_final: 0.7606 (tt) REVERT: C 177 MET cc_start: -0.1537 (mmt) cc_final: -0.2359 (ttt) REVERT: C 240 THR cc_start: 0.7641 (t) cc_final: 0.7400 (m) REVERT: C 245 HIS cc_start: 0.3396 (m-70) cc_final: 0.2962 (m-70) REVERT: C 456 PHE cc_start: 0.6996 (m-80) cc_final: 0.6451 (m-80) REVERT: C 529 LYS cc_start: 0.3614 (tttt) cc_final: 0.3370 (mttp) REVERT: C 614 ASP cc_start: 0.3433 (t0) cc_final: 0.3192 (t0) REVERT: C 740 MET cc_start: 0.5901 (ttm) cc_final: 0.5588 (tpt) REVERT: C 898 PHE cc_start: 0.7262 (t80) cc_final: 0.6832 (t80) REVERT: C 960 ASN cc_start: 0.7203 (m-40) cc_final: 0.6484 (t0) REVERT: C 1029 MET cc_start: 0.7394 (tpp) cc_final: 0.6803 (tpp) REVERT: C 1062 PHE cc_start: 0.7057 (m-10) cc_final: 0.6438 (m-80) REVERT: H 81 MET cc_start: 0.5234 (tmm) cc_final: 0.4988 (tmm) REVERT: H 105 TYR cc_start: 0.6803 (m-80) cc_final: 0.6224 (t80) REVERT: H 220 LYS cc_start: 0.4404 (tttp) cc_final: 0.4051 (pttp) REVERT: H 225 LYS cc_start: 0.0358 (mptt) cc_final: -0.1364 (mttm) outliers start: 2 outliers final: 1 residues processed: 235 average time/residue: 0.1941 time to fit residues: 73.8784 Evaluate side-chains 148 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 21 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 337 optimal weight: 50.0000 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 357 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 149 ASN A 207 HIS A 218 GLN A 388 ASN A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 49 HIS B 501 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 965 GLN B 992 GLN B1011 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN H 182 GLN ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.082583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059842 restraints weight = 218790.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061255 restraints weight = 137826.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062046 restraints weight = 87986.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062350 restraints weight = 66560.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.062451 restraints weight = 60249.385| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 29508 Z= 0.329 Angle : 0.965 13.636 40265 Z= 0.488 Chirality : 0.055 0.464 4636 Planarity : 0.007 0.081 5150 Dihedral : 6.910 52.390 4656 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.95 % Favored : 92.00 % Rotamer: Outliers : 0.25 % Allowed : 6.83 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.73 (0.12), residues: 3600 helix: -0.07 (0.20), residues: 594 sheet: -1.28 (0.18), residues: 749 loop : -2.65 (0.11), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG L 63 TYR 0.033 0.003 TYR H 60 PHE 0.033 0.004 PHE B 490 TRP 0.031 0.003 TRP B 104 HIS 0.013 0.003 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00730 (29425) covalent geometry : angle 0.94531 (40063) SS BOND : bond 0.00901 ( 47) SS BOND : angle 2.30442 ( 94) hydrogen bonds : bond 0.05570 ( 783) hydrogen bonds : angle 6.57267 ( 2183) link_BETA1-4 : bond 0.00386 ( 6) link_BETA1-4 : angle 1.99405 ( 18) link_NAG-ASN : bond 0.00884 ( 30) link_NAG-ASN : angle 3.52395 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.6097 (mt) cc_final: 0.5759 (mt) REVERT: A 92 PHE cc_start: 0.7741 (t80) cc_final: 0.7338 (t80) REVERT: A 117 LEU cc_start: 0.9088 (tt) cc_final: 0.8460 (mt) REVERT: A 200 TYR cc_start: 0.5840 (m-80) cc_final: 0.5233 (m-10) REVERT: A 215 ASP cc_start: 0.4906 (t70) cc_final: 0.4627 (t70) REVERT: A 315 THR cc_start: 0.6764 (p) cc_final: 0.6442 (p) REVERT: A 380 TYR cc_start: 0.6279 (t80) cc_final: 0.6002 (t80) REVERT: A 428 ASP cc_start: 0.6235 (p0) cc_final: 0.5262 (m-30) REVERT: A 1029 MET cc_start: 0.7851 (tpp) cc_final: 0.7635 (tpp) REVERT: A 1041 ASP cc_start: 0.7716 (t0) cc_final: 0.7295 (t0) REVERT: A 1050 MET cc_start: 0.8204 (pmm) cc_final: 0.6868 (pmm) REVERT: B 151 SER cc_start: 0.6800 (p) cc_final: 0.5944 (t) REVERT: B 153 MET cc_start: 0.6679 (mmm) cc_final: 0.5703 (ppp) REVERT: B 177 MET cc_start: -0.2099 (mmt) cc_final: -0.3346 (mtp) REVERT: B 224 GLU cc_start: 0.8974 (pm20) cc_final: 0.8548 (pm20) REVERT: B 421 TYR cc_start: 0.8227 (m-80) cc_final: 0.7852 (m-10) REVERT: B 740 MET cc_start: 0.7830 (ttm) cc_final: 0.7061 (tpp) REVERT: B 1142 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 141 LEU cc_start: 0.8226 (mp) cc_final: 0.8018 (tt) REVERT: C 177 MET cc_start: -0.1550 (mmt) cc_final: -0.2976 (ttt) REVERT: C 245 HIS cc_start: 0.3472 (m-70) cc_final: 0.3132 (m-70) REVERT: C 390 LEU cc_start: 0.6374 (mt) cc_final: 0.5990 (pp) REVERT: C 459 SER cc_start: 0.6038 (p) cc_final: 0.5663 (t) REVERT: C 740 MET cc_start: 0.6147 (ttm) cc_final: 0.5487 (tpt) REVERT: C 902 MET cc_start: 0.7916 (mmm) cc_final: 0.7687 (mmm) REVERT: C 960 ASN cc_start: 0.8155 (m-40) cc_final: 0.6929 (t0) REVERT: C 1029 MET cc_start: 0.7775 (tpp) cc_final: 0.7291 (tpp) REVERT: C 1062 PHE cc_start: 0.7653 (m-10) cc_final: 0.7093 (m-80) REVERT: H 105 TYR cc_start: 0.6791 (m-80) cc_final: 0.5734 (t80) REVERT: H 225 LYS cc_start: 0.0947 (mptt) cc_final: -0.1001 (mttt) outliers start: 7 outliers final: 3 residues processed: 184 average time/residue: 0.1940 time to fit residues: 58.1009 Evaluate side-chains 115 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 147 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 265 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 148 ASN A 149 ASN A 245 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A1002 GLN B 66 HIS B 540 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 992 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 448 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 540 ASN C 613 GLN C 644 GLN C 949 GLN C1088 HIS ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.083869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.062393 restraints weight = 214438.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063275 restraints weight = 142823.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.063608 restraints weight = 101758.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064057 restraints weight = 79946.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064129 restraints weight = 70224.588| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.7754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29508 Z= 0.212 Angle : 0.705 14.995 40265 Z= 0.352 Chirality : 0.048 0.387 4636 Planarity : 0.005 0.060 5150 Dihedral : 6.131 52.437 4656 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.09 % Allowed : 2.62 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.13), residues: 3600 helix: 0.52 (0.21), residues: 598 sheet: -1.36 (0.17), residues: 774 loop : -2.53 (0.11), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 102 TYR 0.022 0.002 TYR A 917 PHE 0.024 0.002 PHE B 906 TRP 0.031 0.002 TRP A 152 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00470 (29425) covalent geometry : angle 0.68510 (40063) SS BOND : bond 0.00422 ( 47) SS BOND : angle 1.70102 ( 94) hydrogen bonds : bond 0.04310 ( 783) hydrogen bonds : angle 6.07835 ( 2183) link_BETA1-4 : bond 0.00513 ( 6) link_BETA1-4 : angle 1.58729 ( 18) link_NAG-ASN : bond 0.00635 ( 30) link_NAG-ASN : angle 3.16705 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.6595 (mt) cc_final: 0.5088 (mt) REVERT: A 92 PHE cc_start: 0.7750 (t80) cc_final: 0.7412 (t80) REVERT: A 117 LEU cc_start: 0.9274 (tt) cc_final: 0.8886 (mt) REVERT: A 200 TYR cc_start: 0.6100 (m-80) cc_final: 0.5498 (m-10) REVERT: A 315 THR cc_start: 0.7305 (p) cc_final: 0.7092 (p) REVERT: A 380 TYR cc_start: 0.6161 (t80) cc_final: 0.5879 (t80) REVERT: A 428 ASP cc_start: 0.5470 (p0) cc_final: 0.5063 (m-30) REVERT: A 584 ILE cc_start: 0.7466 (mm) cc_final: 0.7210 (mm) REVERT: A 697 MET cc_start: 0.8696 (tpp) cc_final: 0.7950 (tpt) REVERT: A 1041 ASP cc_start: 0.7804 (t0) cc_final: 0.7461 (t0) REVERT: A 1050 MET cc_start: 0.8181 (pmm) cc_final: 0.7502 (pmm) REVERT: B 151 SER cc_start: 0.6809 (p) cc_final: 0.6024 (t) REVERT: B 153 MET cc_start: 0.6751 (mmm) cc_final: 0.6149 (ppp) REVERT: B 177 MET cc_start: -0.1924 (mmt) cc_final: -0.2555 (mtp) REVERT: B 224 GLU cc_start: 0.9008 (pm20) cc_final: 0.8665 (pm20) REVERT: B 740 MET cc_start: 0.7435 (ttm) cc_final: 0.7054 (tpp) REVERT: B 900 MET cc_start: 0.8663 (mtp) cc_final: 0.8273 (mtp) REVERT: B 1130 ILE cc_start: 0.7795 (pt) cc_final: 0.7558 (mt) REVERT: C 55 PHE cc_start: 0.7531 (m-10) cc_final: 0.6950 (m-80) REVERT: C 141 LEU cc_start: 0.8679 (mp) cc_final: 0.8455 (tt) REVERT: C 177 MET cc_start: -0.1251 (mmt) cc_final: -0.2625 (ttt) REVERT: C 245 HIS cc_start: 0.4200 (m-70) cc_final: 0.3960 (m-70) REVERT: C 740 MET cc_start: 0.5985 (ttm) cc_final: 0.5464 (tpt) REVERT: C 960 ASN cc_start: 0.8057 (m-40) cc_final: 0.7049 (t0) REVERT: C 1005 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6980 (mm-40) REVERT: C 1029 MET cc_start: 0.7594 (tpp) cc_final: 0.7257 (tpp) REVERT: C 1062 PHE cc_start: 0.6996 (m-10) cc_final: 0.6770 (m-10) REVERT: H 105 TYR cc_start: 0.6775 (m-80) cc_final: 0.5850 (t80) REVERT: H 225 LYS cc_start: 0.1103 (mptt) cc_final: -0.0838 (mttt) outliers start: 2 outliers final: 1 residues processed: 165 average time/residue: 0.1852 time to fit residues: 50.5499 Evaluate side-chains 107 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 154 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 349 optimal weight: 0.5980 chunk 272 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 224 optimal weight: 20.0000 chunk 175 optimal weight: 0.0270 chunk 67 optimal weight: 0.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 66 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 125 ASN H 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.085472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064100 restraints weight = 255087.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064351 restraints weight = 188756.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064782 restraints weight = 129834.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064756 restraints weight = 114656.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.065174 restraints weight = 101570.388| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29508 Z= 0.110 Angle : 0.577 15.439 40265 Z= 0.285 Chirality : 0.046 0.355 4636 Planarity : 0.004 0.070 5150 Dihedral : 5.076 47.069 4656 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.05 (0.13), residues: 3600 helix: 1.27 (0.22), residues: 581 sheet: -0.96 (0.17), residues: 783 loop : -2.38 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.015 0.001 TYR B 756 PHE 0.024 0.001 PHE B 275 TRP 0.019 0.001 TRP B 64 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00244 (29425) covalent geometry : angle 0.55994 (40063) SS BOND : bond 0.00341 ( 47) SS BOND : angle 1.37644 ( 94) hydrogen bonds : bond 0.03437 ( 783) hydrogen bonds : angle 5.42456 ( 2183) link_BETA1-4 : bond 0.00327 ( 6) link_BETA1-4 : angle 1.28786 ( 18) link_NAG-ASN : bond 0.00479 ( 30) link_NAG-ASN : angle 2.63198 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7721 (t80) cc_final: 0.7328 (t80) REVERT: A 117 LEU cc_start: 0.9294 (tt) cc_final: 0.8852 (mt) REVERT: A 200 TYR cc_start: 0.6024 (m-80) cc_final: 0.5455 (m-10) REVERT: A 380 TYR cc_start: 0.6372 (t80) cc_final: 0.6132 (t80) REVERT: A 428 ASP cc_start: 0.5004 (p0) cc_final: 0.4456 (m-30) REVERT: A 697 MET cc_start: 0.8617 (tpp) cc_final: 0.7785 (tpt) REVERT: A 731 MET cc_start: 0.7206 (ptm) cc_final: 0.6543 (ppp) REVERT: A 1041 ASP cc_start: 0.7695 (t0) cc_final: 0.7286 (t0) REVERT: A 1050 MET cc_start: 0.8072 (pmm) cc_final: 0.7287 (pmm) REVERT: B 151 SER cc_start: 0.7195 (p) cc_final: 0.6142 (t) REVERT: B 153 MET cc_start: 0.6790 (mmm) cc_final: 0.6056 (ppp) REVERT: B 177 MET cc_start: -0.0655 (mmt) cc_final: -0.1370 (mtp) REVERT: B 224 GLU cc_start: 0.8878 (pm20) cc_final: 0.8509 (pm20) REVERT: B 421 TYR cc_start: 0.7410 (m-10) cc_final: 0.6813 (m-10) REVERT: B 505 TYR cc_start: 0.5143 (m-10) cc_final: 0.4888 (m-10) REVERT: B 740 MET cc_start: 0.7199 (ttm) cc_final: 0.6880 (tpp) REVERT: B 1130 ILE cc_start: 0.7891 (pt) cc_final: 0.7690 (mt) REVERT: C 124 THR cc_start: 0.6487 (p) cc_final: 0.6236 (p) REVERT: C 141 LEU cc_start: 0.8583 (mp) cc_final: 0.8327 (tt) REVERT: C 177 MET cc_start: -0.1239 (mmt) cc_final: -0.1441 (ttm) REVERT: C 245 HIS cc_start: 0.4344 (m-70) cc_final: 0.4050 (m-70) REVERT: C 740 MET cc_start: 0.6088 (ttm) cc_final: 0.5417 (tpt) REVERT: C 960 ASN cc_start: 0.7901 (m-40) cc_final: 0.6962 (t0) REVERT: C 1005 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7134 (mm-40) REVERT: C 1029 MET cc_start: 0.7409 (tpp) cc_final: 0.7156 (tpp) REVERT: H 81 MET cc_start: 0.5291 (tmm) cc_final: 0.5029 (tmm) REVERT: H 105 TYR cc_start: 0.6625 (m-80) cc_final: 0.5710 (t80) REVERT: H 225 LYS cc_start: 0.0954 (mptt) cc_final: -0.1026 (mttt) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.1824 time to fit residues: 47.9158 Evaluate side-chains 103 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 978 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1011 GLN C 218 GLN C 501 ASN C 544 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.081155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.058578 restraints weight = 228356.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.058997 restraints weight = 154266.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059923 restraints weight = 110593.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.060120 restraints weight = 74660.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060276 restraints weight = 70714.026| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.8641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 29508 Z= 0.218 Angle : 0.728 15.161 40265 Z= 0.363 Chirality : 0.049 0.400 4636 Planarity : 0.005 0.090 5150 Dihedral : 5.916 59.260 4656 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.23 (0.13), residues: 3600 helix: 0.73 (0.21), residues: 590 sheet: -1.06 (0.17), residues: 787 loop : -2.40 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 63 TYR 0.021 0.002 TYR B 313 PHE 0.028 0.002 PHE C 759 TRP 0.021 0.002 TRP C 886 HIS 0.008 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00488 (29425) covalent geometry : angle 0.71011 (40063) SS BOND : bond 0.00694 ( 47) SS BOND : angle 1.65508 ( 94) hydrogen bonds : bond 0.04249 ( 783) hydrogen bonds : angle 5.90242 ( 2183) link_BETA1-4 : bond 0.00634 ( 6) link_BETA1-4 : angle 1.65788 ( 18) link_NAG-ASN : bond 0.00619 ( 30) link_NAG-ASN : angle 3.01909 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7789 (t80) cc_final: 0.7346 (t80) REVERT: A 117 LEU cc_start: 0.9188 (tt) cc_final: 0.8575 (mt) REVERT: A 200 TYR cc_start: 0.5958 (m-80) cc_final: 0.5394 (m-10) REVERT: A 215 ASP cc_start: 0.4288 (t70) cc_final: 0.3933 (t70) REVERT: A 380 TYR cc_start: 0.6344 (t80) cc_final: 0.6103 (t80) REVERT: A 428 ASP cc_start: 0.5375 (p0) cc_final: 0.4622 (m-30) REVERT: A 584 ILE cc_start: 0.7516 (mm) cc_final: 0.7012 (mm) REVERT: A 697 MET cc_start: 0.8550 (tpp) cc_final: 0.7402 (tpt) REVERT: A 731 MET cc_start: 0.7344 (ptm) cc_final: 0.6782 (ppp) REVERT: A 1029 MET cc_start: 0.8454 (tpp) cc_final: 0.7878 (tpp) REVERT: A 1041 ASP cc_start: 0.7905 (t0) cc_final: 0.7396 (t0) REVERT: A 1050 MET cc_start: 0.8029 (pmm) cc_final: 0.6746 (pmm) REVERT: B 151 SER cc_start: 0.6802 (p) cc_final: 0.6091 (t) REVERT: B 153 MET cc_start: 0.6859 (mmm) cc_final: 0.6172 (ppp) REVERT: B 177 MET cc_start: -0.1608 (mmt) cc_final: -0.2426 (mtp) REVERT: B 224 GLU cc_start: 0.9049 (pm20) cc_final: 0.8710 (pm20) REVERT: B 523 THR cc_start: 0.5917 (p) cc_final: 0.5590 (t) REVERT: B 1029 MET cc_start: 0.7807 (ttm) cc_final: 0.7508 (ttm) REVERT: C 177 MET cc_start: -0.0953 (mmt) cc_final: -0.2178 (ttt) REVERT: C 245 HIS cc_start: 0.4169 (m-70) cc_final: 0.3803 (m-70) REVERT: C 740 MET cc_start: 0.5961 (ttm) cc_final: 0.5236 (tpt) REVERT: C 1029 MET cc_start: 0.7386 (tpp) cc_final: 0.6661 (tpp) REVERT: C 1033 VAL cc_start: 0.8311 (t) cc_final: 0.7310 (t) REVERT: H 105 TYR cc_start: 0.6818 (m-80) cc_final: 0.5656 (t80) REVERT: H 225 LYS cc_start: 0.1054 (mptt) cc_final: -0.0987 (mttm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1787 time to fit residues: 43.2082 Evaluate side-chains 100 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 208 optimal weight: 4.9990 chunk 352 optimal weight: 30.0000 chunk 251 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 263 optimal weight: 0.3980 chunk 274 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 437 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 185 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.080543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058358 restraints weight = 214943.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058838 restraints weight = 145165.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059329 restraints weight = 104322.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059558 restraints weight = 78889.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059681 restraints weight = 73007.341| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.9156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29508 Z= 0.194 Angle : 0.672 15.962 40265 Z= 0.337 Chirality : 0.048 0.379 4636 Planarity : 0.005 0.080 5150 Dihedral : 5.963 50.436 4656 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.20 (0.13), residues: 3600 helix: 0.92 (0.21), residues: 582 sheet: -1.03 (0.18), residues: 778 loop : -2.42 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 328 TYR 0.019 0.002 TYR C 266 PHE 0.020 0.002 PHE C 133 TRP 0.055 0.002 TRP C 64 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00433 (29425) covalent geometry : angle 0.65309 (40063) SS BOND : bond 0.00400 ( 47) SS BOND : angle 1.65753 ( 94) hydrogen bonds : bond 0.03944 ( 783) hydrogen bonds : angle 5.88313 ( 2183) link_BETA1-4 : bond 0.00630 ( 6) link_BETA1-4 : angle 1.45471 ( 18) link_NAG-ASN : bond 0.00586 ( 30) link_NAG-ASN : angle 2.93803 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7706 (t80) cc_final: 0.7349 (t80) REVERT: A 177 MET cc_start: -0.0453 (mmt) cc_final: -0.0698 (mmt) REVERT: A 200 TYR cc_start: 0.6220 (m-80) cc_final: 0.5537 (m-10) REVERT: A 380 TYR cc_start: 0.6461 (t80) cc_final: 0.6253 (t80) REVERT: A 428 ASP cc_start: 0.5429 (p0) cc_final: 0.4713 (m-30) REVERT: A 584 ILE cc_start: 0.7736 (mm) cc_final: 0.7241 (mm) REVERT: A 697 MET cc_start: 0.8774 (tpp) cc_final: 0.7952 (tpt) REVERT: A 731 MET cc_start: 0.7234 (ptm) cc_final: 0.6788 (ppp) REVERT: A 1041 ASP cc_start: 0.7850 (t0) cc_final: 0.7372 (t0) REVERT: A 1050 MET cc_start: 0.7973 (pmm) cc_final: 0.7122 (pmm) REVERT: B 153 MET cc_start: 0.6841 (mmm) cc_final: 0.6226 (ppp) REVERT: B 224 GLU cc_start: 0.8983 (pm20) cc_final: 0.8679 (pm20) REVERT: B 740 MET cc_start: 0.7593 (tpp) cc_final: 0.7314 (tpp) REVERT: B 919 ASN cc_start: 0.6845 (p0) cc_final: 0.6123 (m-40) REVERT: B 1001 LEU cc_start: 0.8872 (mt) cc_final: 0.8623 (mt) REVERT: B 1005 GLN cc_start: 0.5895 (mt0) cc_final: 0.5660 (mt0) REVERT: C 55 PHE cc_start: 0.6477 (m-10) cc_final: 0.6233 (m-80) REVERT: C 177 MET cc_start: -0.0792 (mmt) cc_final: -0.2249 (ttm) REVERT: C 245 HIS cc_start: 0.4436 (m-70) cc_final: 0.4051 (m-70) REVERT: C 357 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7893 (ttt90) REVERT: C 740 MET cc_start: 0.6208 (ttm) cc_final: 0.5263 (tpt) REVERT: C 1029 MET cc_start: 0.7438 (tpp) cc_final: 0.6666 (tpp) REVERT: C 1033 VAL cc_start: 0.8357 (t) cc_final: 0.7438 (t) REVERT: H 105 TYR cc_start: 0.6861 (m-80) cc_final: 0.5684 (t80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1790 time to fit residues: 42.3265 Evaluate side-chains 95 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 158 optimal weight: 2.9990 chunk 118 optimal weight: 30.0000 chunk 303 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.081601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059038 restraints weight = 257995.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059952 restraints weight = 162843.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060343 restraints weight = 108023.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060539 restraints weight = 90298.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060678 restraints weight = 77663.230| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.9130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29508 Z= 0.116 Angle : 0.624 22.658 40265 Z= 0.301 Chirality : 0.046 0.359 4636 Planarity : 0.005 0.076 5150 Dihedral : 5.615 57.702 4656 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -1.94 (0.13), residues: 3600 helix: 1.35 (0.22), residues: 574 sheet: -0.79 (0.18), residues: 766 loop : -2.33 (0.12), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 44 TYR 0.019 0.001 TYR C 873 PHE 0.027 0.001 PHE B 906 TRP 0.034 0.002 TRP C 64 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00261 (29425) covalent geometry : angle 0.59431 (40063) SS BOND : bond 0.00305 ( 47) SS BOND : angle 1.40205 ( 94) hydrogen bonds : bond 0.03497 ( 783) hydrogen bonds : angle 5.45287 ( 2183) link_BETA1-4 : bond 0.00642 ( 6) link_BETA1-4 : angle 1.22687 ( 18) link_NAG-ASN : bond 0.00673 ( 30) link_NAG-ASN : angle 3.83718 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7711 (t80) cc_final: 0.6867 (t80) REVERT: A 117 LEU cc_start: 0.9126 (tt) cc_final: 0.8417 (mt) REVERT: A 177 MET cc_start: 0.0120 (mmt) cc_final: -0.0086 (mmt) REVERT: A 200 TYR cc_start: 0.6192 (m-80) cc_final: 0.5562 (m-10) REVERT: A 380 TYR cc_start: 0.6567 (t80) cc_final: 0.6330 (t80) REVERT: A 428 ASP cc_start: 0.5445 (p0) cc_final: 0.4690 (m-30) REVERT: A 584 ILE cc_start: 0.7637 (mm) cc_final: 0.7107 (mm) REVERT: A 731 MET cc_start: 0.7419 (ptm) cc_final: 0.7143 (ppp) REVERT: A 913 GLN cc_start: 0.8148 (pp30) cc_final: 0.7924 (pp30) REVERT: A 1041 ASP cc_start: 0.7418 (t0) cc_final: 0.7033 (t0) REVERT: A 1050 MET cc_start: 0.7994 (pmm) cc_final: 0.7154 (pmm) REVERT: B 153 MET cc_start: 0.6858 (mmm) cc_final: 0.6144 (ppp) REVERT: B 224 GLU cc_start: 0.8844 (pm20) cc_final: 0.8642 (pm20) REVERT: B 740 MET cc_start: 0.7459 (tpp) cc_final: 0.7111 (tpp) REVERT: B 919 ASN cc_start: 0.6787 (p0) cc_final: 0.6080 (m-40) REVERT: B 1001 LEU cc_start: 0.8847 (mt) cc_final: 0.8607 (mt) REVERT: B 1029 MET cc_start: 0.7789 (ttm) cc_final: 0.7505 (ttm) REVERT: C 177 MET cc_start: -0.1006 (mmt) cc_final: -0.2613 (ttt) REVERT: C 245 HIS cc_start: 0.4423 (m-70) cc_final: 0.4061 (m-70) REVERT: C 357 ARG cc_start: 0.8001 (ttt-90) cc_final: 0.7762 (ttt90) REVERT: C 740 MET cc_start: 0.6247 (ttm) cc_final: 0.5278 (tpt) REVERT: C 1005 GLN cc_start: 0.7304 (mm-40) cc_final: 0.7076 (mm-40) REVERT: C 1029 MET cc_start: 0.7372 (tpp) cc_final: 0.6751 (tpp) REVERT: C 1033 VAL cc_start: 0.8272 (t) cc_final: 0.7341 (t) REVERT: H 105 TYR cc_start: 0.6688 (m-80) cc_final: 0.5587 (t80) REVERT: H 158 PRO cc_start: -0.1655 (Cg_endo) cc_final: -0.2077 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1853 time to fit residues: 45.3551 Evaluate side-chains 106 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 254 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A1054 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 751 ASN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.080290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058209 restraints weight = 239121.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058682 restraints weight = 159501.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059055 restraints weight = 107774.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059201 restraints weight = 96934.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059302 restraints weight = 83754.329| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.9470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29508 Z= 0.170 Angle : 0.659 15.346 40265 Z= 0.325 Chirality : 0.047 0.369 4636 Planarity : 0.005 0.070 5150 Dihedral : 6.165 93.868 4656 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -1.99 (0.13), residues: 3600 helix: 1.06 (0.22), residues: 586 sheet: -0.78 (0.18), residues: 765 loop : -2.32 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 44 TYR 0.031 0.002 TYR B 495 PHE 0.032 0.002 PHE B 906 TRP 0.032 0.002 TRP C 64 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00383 (29425) covalent geometry : angle 0.63806 (40063) SS BOND : bond 0.00376 ( 47) SS BOND : angle 1.50189 ( 94) hydrogen bonds : bond 0.03705 ( 783) hydrogen bonds : angle 5.58165 ( 2183) link_BETA1-4 : bond 0.00511 ( 6) link_BETA1-4 : angle 1.41465 ( 18) link_NAG-ASN : bond 0.00550 ( 30) link_NAG-ASN : angle 3.18711 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7735 (t80) cc_final: 0.6891 (t80) REVERT: A 177 MET cc_start: -0.0672 (mmt) cc_final: -0.0904 (mmt) REVERT: A 200 TYR cc_start: 0.5973 (m-80) cc_final: 0.5557 (m-10) REVERT: A 380 TYR cc_start: 0.6495 (t80) cc_final: 0.6268 (t80) REVERT: A 428 ASP cc_start: 0.5493 (p0) cc_final: 0.4749 (m-30) REVERT: A 584 ILE cc_start: 0.7770 (mm) cc_final: 0.7268 (mm) REVERT: A 697 MET cc_start: 0.8028 (tpt) cc_final: 0.7114 (tpt) REVERT: A 731 MET cc_start: 0.7374 (ptm) cc_final: 0.7028 (ppp) REVERT: A 1041 ASP cc_start: 0.7609 (t0) cc_final: 0.7241 (t0) REVERT: A 1050 MET cc_start: 0.8172 (pmm) cc_final: 0.7303 (pmm) REVERT: B 153 MET cc_start: 0.6835 (mmm) cc_final: 0.6200 (ppp) REVERT: B 740 MET cc_start: 0.7582 (tpp) cc_final: 0.7305 (tpp) REVERT: B 919 ASN cc_start: 0.6947 (p0) cc_final: 0.6019 (m-40) REVERT: B 1001 LEU cc_start: 0.8913 (mt) cc_final: 0.8601 (mt) REVERT: B 1005 GLN cc_start: 0.6046 (mt0) cc_final: 0.5773 (mt0) REVERT: B 1029 MET cc_start: 0.7561 (ttm) cc_final: 0.7338 (ttm) REVERT: C 55 PHE cc_start: 0.7122 (m-80) cc_final: 0.6777 (m-80) REVERT: C 177 MET cc_start: -0.0857 (mmt) cc_final: -0.2504 (ttt) REVERT: C 245 HIS cc_start: 0.4530 (m-70) cc_final: 0.4155 (m-70) REVERT: C 357 ARG cc_start: 0.8012 (ttt-90) cc_final: 0.7654 (ttt90) REVERT: C 740 MET cc_start: 0.5870 (ttm) cc_final: 0.5313 (tpt) REVERT: C 1005 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7027 (mm-40) REVERT: C 1029 MET cc_start: 0.7312 (tpp) cc_final: 0.6791 (tpp) REVERT: C 1033 VAL cc_start: 0.8391 (t) cc_final: 0.7421 (t) REVERT: H 105 TYR cc_start: 0.6781 (m-80) cc_final: 0.5640 (t80) REVERT: H 158 PRO cc_start: 0.1166 (Cg_endo) cc_final: 0.0714 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1726 time to fit residues: 38.8421 Evaluate side-chains 101 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 222 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 40 optimal weight: 0.0570 chunk 281 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 297 optimal weight: 0.9980 chunk 259 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 211 ASN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.082893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061924 restraints weight = 243441.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061999 restraints weight = 174909.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062298 restraints weight = 126450.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062446 restraints weight = 110328.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.062643 restraints weight = 99961.766| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.9386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29508 Z= 0.102 Angle : 0.580 14.935 40265 Z= 0.284 Chirality : 0.046 0.341 4636 Planarity : 0.004 0.076 5150 Dihedral : 5.734 102.434 4656 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -1.69 (0.14), residues: 3600 helix: 1.58 (0.22), residues: 565 sheet: -0.49 (0.18), residues: 794 loop : -2.23 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 63 TYR 0.016 0.001 TYR A 873 PHE 0.024 0.001 PHE B 906 TRP 0.024 0.001 TRP C 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00228 (29425) covalent geometry : angle 0.56142 (40063) SS BOND : bond 0.00316 ( 47) SS BOND : angle 1.31282 ( 94) hydrogen bonds : bond 0.03290 ( 783) hydrogen bonds : angle 5.19705 ( 2183) link_BETA1-4 : bond 0.00526 ( 6) link_BETA1-4 : angle 1.09389 ( 18) link_NAG-ASN : bond 0.00544 ( 30) link_NAG-ASN : angle 2.85221 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4956.21 seconds wall clock time: 86 minutes 55.75 seconds (5215.75 seconds total)