Starting phenix.real_space_refine on Thu Mar 5 16:16:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdk_22825/03_2026/7kdk_22825.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdk_22825/03_2026/7kdk_22825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kdk_22825/03_2026/7kdk_22825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdk_22825/03_2026/7kdk_22825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kdk_22825/03_2026/7kdk_22825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdk_22825/03_2026/7kdk_22825.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 15084 2.51 5 N 3852 2.21 5 O 4653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.02s 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: 23688 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "B" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" 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: "P" 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: "Q" 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: "R" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.48, per 1000 atoms: 0.23 Number of scatterers: 23688 At special positions: 0 Unit cell: (128.018, 135.424, 170.338, 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 99 16.00 O 4653 8.00 N 3852 7.00 C 15084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.02 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=1.94 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 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=2.04 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=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C 717 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 975.0 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5478 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 45 sheets defined 27.8% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.977A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.769A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.222A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.613A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.934A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.661A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.534A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.868A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.305A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.604A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.955A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.854A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.501A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.529A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.589A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.562A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.611A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.781A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.164A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.383A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.241A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.734A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.038A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.984A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.658A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.531A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.224A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.222A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.526A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.806A 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: 5.853A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.528A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.752A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.620A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.818A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.500A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.177A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.409A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.171A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.725A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.149A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.797A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.667A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.332A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.547A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.746A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.616A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.530A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.223A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.468A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.470A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.832A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.733A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.536A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.851A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.374A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.746A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.521A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.190A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.369A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.592A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.78 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5912 1.33 - 1.46: 4926 1.46 - 1.58: 13225 1.58 - 1.70: 0 1.70 - 1.83: 123 Bond restraints: 24186 Sorted by residual: bond pdb=" CA ALA A 520 " pdb=" C ALA A 520 " ideal model delta sigma weight residual 1.518 1.558 -0.040 9.60e-03 1.09e+04 1.73e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 24181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 28510 2.70 - 5.39: 4250 5.39 - 8.09: 117 8.09 - 10.79: 2 10.79 - 13.49: 7 Bond angle restraints: 32886 Sorted by residual: angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 111.54 125.03 -13.49 1.36e+00 5.41e-01 9.83e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 120.03 -11.07 1.49e+00 4.50e-01 5.52e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 108.96 119.97 -11.01 1.49e+00 4.50e-01 5.46e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 109.07 120.24 -11.17 1.52e+00 4.33e-01 5.40e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.74 -6.14 1.00e+00 1.00e+00 3.77e+01 ... (remaining 32881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14194 17.94 - 35.87: 825 35.87 - 53.81: 117 53.81 - 71.75: 48 71.75 - 89.68: 29 Dihedral angle restraints: 15213 sinusoidal: 6729 harmonic: 8484 Sorted by residual: dihedral pdb=" C ASN A 99 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" CB ASN A 99 " ideal model delta harmonic sigma weight residual -122.60 -150.74 28.14 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CA ASN A 99 " pdb=" CB ASN A 99 " ideal model delta harmonic sigma weight residual 122.80 148.96 -26.16 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -174.95 88.95 1 1.00e+01 1.00e-02 9.42e+01 ... (remaining 15210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 3888 0.237 - 0.474: 56 0.474 - 0.710: 3 0.710 - 0.947: 0 0.947 - 1.184: 1 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.73e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.73e+01 ... (remaining 3945 not shown) Planarity restraints: 4203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.235 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" CG ASN A 165 " -0.164 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.429 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " 0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.211 2.00e-02 2.50e+03 2.53e-01 7.98e+02 pdb=" CG ASN A 61 " 0.126 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.408 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.303 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " 0.195 2.00e-02 2.50e+03 2.13e-01 5.67e+02 pdb=" CG ASN C 165 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " -0.329 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " 0.259 2.00e-02 2.50e+03 ... (remaining 4200 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 10833 2.97 - 3.45: 22502 3.45 - 3.94: 40196 3.94 - 4.42: 44994 4.42 - 4.90: 76179 Nonbonded interactions: 194704 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.490 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.495 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.513 3.040 nonbonded pdb=" OG SER C 591 " pdb=" OE1 GLU C 619 " model vdw 2.535 3.040 ... (remaining 194699 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: 0.02 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.840 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: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.014 0.087 24285 Z= 0.795 Angle : 1.813 13.487 33147 Z= 1.196 Chirality : 0.102 1.184 3948 Planarity : 0.014 0.186 4155 Dihedral : 12.359 89.682 9627 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 0.12 % Allowed : 0.90 % Favored : 98.98 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 2844 helix: -0.60 (0.17), residues: 672 sheet: -0.08 (0.19), residues: 591 loop : -0.84 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1019 TYR 0.145 0.022 TYR C 495 PHE 0.132 0.014 PHE A 718 TRP 0.118 0.026 TRP B 104 HIS 0.010 0.003 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.01394 (24186) covalent geometry : angle 1.78418 (32886) SS BOND : bond 0.01890 ( 36) SS BOND : angle 2.52929 ( 72) hydrogen bonds : bond 0.14022 ( 1029) hydrogen bonds : angle 8.14526 ( 2814) link_BETA1-4 : bond 0.02586 ( 15) link_BETA1-4 : angle 4.68550 ( 45) link_NAG-ASN : bond 0.01237 ( 48) link_NAG-ASN : angle 4.46634 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 394 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 397 average time/residue: 0.5444 time to fit residues: 252.2749 Evaluate side-chains 207 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1101 HIS B 314 GLN B 321 GLN B 360 ASN B 394 ASN C 207 HIS C 314 GLN C 360 ASN C 564 GLN C 675 GLN C 751 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.190832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124317 restraints weight = 28514.295| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.13 r_work: 0.3526 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 24285 Z= 0.167 Angle : 0.784 26.771 33147 Z= 0.383 Chirality : 0.048 0.295 3948 Planarity : 0.004 0.042 4155 Dihedral : 6.020 54.399 4426 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.08 % Allowed : 7.95 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 2844 helix: 1.17 (0.20), residues: 642 sheet: -0.04 (0.19), residues: 615 loop : -0.51 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.033 0.002 TYR A 508 PHE 0.023 0.002 PHE B 58 TRP 0.016 0.002 TRP A 64 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00376 (24186) covalent geometry : angle 0.70659 (32886) SS BOND : bond 0.00767 ( 36) SS BOND : angle 2.92903 ( 72) hydrogen bonds : bond 0.04445 ( 1029) hydrogen bonds : angle 6.42600 ( 2814) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 1.81869 ( 45) link_NAG-ASN : bond 0.00354 ( 48) link_NAG-ASN : angle 4.70143 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 424 LYS cc_start: 0.7778 (tptt) cc_final: 0.6549 (mttt) REVERT: A 514 SER cc_start: 0.8620 (t) cc_final: 0.8388 (m) REVERT: A 529 LYS cc_start: 0.8277 (mppt) cc_final: 0.7914 (tmtm) REVERT: A 532 ASN cc_start: 0.8505 (t0) cc_final: 0.8206 (t0) REVERT: A 957 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: A 988 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 202 LYS cc_start: 0.7335 (mttm) cc_final: 0.7127 (mttm) REVERT: B 237 ARG cc_start: 0.6638 (mmm-85) cc_final: 0.6108 (mtp180) REVERT: B 319 ARG cc_start: 0.8346 (ptp-170) cc_final: 0.7458 (ptm160) REVERT: B 356 LYS cc_start: 0.8196 (tttp) cc_final: 0.7985 (tttt) REVERT: B 424 LYS cc_start: 0.7627 (tptt) cc_final: 0.7282 (tppp) REVERT: B 556 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.7045 (p0) REVERT: B 663 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8519 (t0) REVERT: B 900 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: B 902 MET cc_start: 0.8525 (mmm) cc_final: 0.8315 (mmt) REVERT: B 988 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 1092 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: B 1101 HIS cc_start: 0.7978 (m90) cc_final: 0.7649 (m90) REVERT: C 128 ILE cc_start: 0.6413 (mt) cc_final: 0.5815 (mp) REVERT: C 356 LYS cc_start: 0.8079 (tttp) cc_final: 0.7841 (tttt) REVERT: C 400 PHE cc_start: 0.8184 (p90) cc_final: 0.7983 (p90) REVERT: C 424 LYS cc_start: 0.7319 (tptp) cc_final: 0.6657 (mttt) REVERT: C 463 PRO cc_start: 0.8799 (Cg_exo) cc_final: 0.8298 (Cg_endo) REVERT: C 556 ASN cc_start: 0.7854 (m-40) cc_final: 0.7408 (p0) REVERT: C 582 LEU cc_start: 0.8578 (mt) cc_final: 0.8375 (mm) REVERT: C 586 ASP cc_start: 0.7407 (m-30) cc_final: 0.7077 (m-30) REVERT: C 964 LYS cc_start: 0.8701 (mttt) cc_final: 0.8287 (mmmt) REVERT: C 1091 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7707 (mtt-85) outliers start: 53 outliers final: 19 residues processed: 289 average time/residue: 0.5254 time to fit residues: 178.6287 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 519 HIS A 675 GLN A1010 GLN B 334 ASN B 360 ASN B1010 GLN C 314 GLN C 360 ASN C 394 ASN C 519 HIS C1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.188676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122286 restraints weight = 28647.352| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.13 r_work: 0.3473 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 24285 Z= 0.203 Angle : 0.680 12.063 33147 Z= 0.341 Chirality : 0.047 0.230 3948 Planarity : 0.004 0.038 4155 Dihedral : 5.634 56.690 4422 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.31 % Allowed : 9.71 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2844 helix: 1.27 (0.20), residues: 639 sheet: 0.03 (0.19), residues: 588 loop : -0.48 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.023 0.002 TYR B 265 PHE 0.022 0.002 PHE B1121 TRP 0.010 0.002 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00489 (24186) covalent geometry : angle 0.64099 (32886) SS BOND : bond 0.00687 ( 36) SS BOND : angle 2.51178 ( 72) hydrogen bonds : bond 0.04226 ( 1029) hydrogen bonds : angle 6.14297 ( 2814) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.54162 ( 45) link_NAG-ASN : bond 0.00274 ( 48) link_NAG-ASN : angle 2.94742 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7837 (m-80) cc_final: 0.7590 (m-10) REVERT: A 357 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7645 (tpt-90) REVERT: A 424 LYS cc_start: 0.7827 (tptt) cc_final: 0.6597 (mttp) REVERT: A 514 SER cc_start: 0.8683 (t) cc_final: 0.8447 (m) REVERT: A 529 LYS cc_start: 0.8229 (mppt) cc_final: 0.7869 (tttp) REVERT: A 532 ASN cc_start: 0.8529 (t0) cc_final: 0.8229 (t0) REVERT: A 646 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8115 (ttm110) REVERT: A 825 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8322 (mttp) REVERT: A 900 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8424 (mtp) REVERT: A 957 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 994 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: B 202 LYS cc_start: 0.7382 (mttm) cc_final: 0.6839 (mptt) REVERT: B 237 ARG cc_start: 0.6772 (mmm-85) cc_final: 0.6287 (mtp180) REVERT: B 319 ARG cc_start: 0.8384 (ptp-170) cc_final: 0.7462 (ptm160) REVERT: B 356 LYS cc_start: 0.8169 (tttp) cc_final: 0.7927 (tttt) REVERT: B 424 LYS cc_start: 0.7611 (tptt) cc_final: 0.7310 (tppp) REVERT: B 508 TYR cc_start: 0.7849 (m-80) cc_final: 0.7468 (m-80) REVERT: B 556 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7144 (p0) REVERT: B 900 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: B 988 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 1092 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: B 1101 HIS cc_start: 0.8083 (m90) cc_final: 0.7838 (m90) REVERT: C 356 LYS cc_start: 0.8173 (tttp) cc_final: 0.7957 (tttt) REVERT: C 400 PHE cc_start: 0.8318 (p90) cc_final: 0.8058 (p90) REVERT: C 424 LYS cc_start: 0.7420 (tptp) cc_final: 0.6691 (mttt) REVERT: C 463 PRO cc_start: 0.8792 (Cg_exo) cc_final: 0.8318 (Cg_endo) REVERT: C 582 LEU cc_start: 0.8667 (mt) cc_final: 0.8435 (mm) REVERT: C 586 ASP cc_start: 0.7333 (m-30) cc_final: 0.7018 (m-30) REVERT: C 964 LYS cc_start: 0.8737 (mttt) cc_final: 0.8362 (mmmt) outliers start: 59 outliers final: 28 residues processed: 258 average time/residue: 0.5247 time to fit residues: 159.1581 Evaluate side-chains 226 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 360 ASN A1135 ASN B 207 HIS B 334 ASN B 360 ASN B 564 GLN B1106 GLN C 314 GLN C 360 ASN C 755 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.187484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121095 restraints weight = 28455.723| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.12 r_work: 0.3457 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24285 Z= 0.228 Angle : 0.675 14.083 33147 Z= 0.338 Chirality : 0.047 0.208 3948 Planarity : 0.004 0.041 4155 Dihedral : 5.458 56.475 4422 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.74 % Allowed : 10.61 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 2844 helix: 1.17 (0.20), residues: 654 sheet: -0.17 (0.19), residues: 579 loop : -0.40 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 408 TYR 0.025 0.002 TYR A 508 PHE 0.025 0.002 PHE B1121 TRP 0.010 0.002 TRP B1102 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00545 (24186) covalent geometry : angle 0.64038 (32886) SS BOND : bond 0.00573 ( 36) SS BOND : angle 2.70575 ( 72) hydrogen bonds : bond 0.04170 ( 1029) hydrogen bonds : angle 6.12528 ( 2814) link_BETA1-4 : bond 0.00232 ( 15) link_BETA1-4 : angle 1.41385 ( 45) link_NAG-ASN : bond 0.00626 ( 48) link_NAG-ASN : angle 2.65690 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 211 time to evaluate : 0.840 Fit side-chains REVERT: A 32 PHE cc_start: 0.7877 (m-80) cc_final: 0.7645 (m-10) REVERT: A 190 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7708 (ttp80) REVERT: A 367 VAL cc_start: 0.9112 (t) cc_final: 0.8836 (m) REVERT: A 392 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7094 (m-80) REVERT: A 424 LYS cc_start: 0.7838 (tptt) cc_final: 0.6434 (mttp) REVERT: A 514 SER cc_start: 0.8775 (t) cc_final: 0.8229 (m) REVERT: A 529 LYS cc_start: 0.8290 (mppt) cc_final: 0.7885 (tttp) REVERT: A 646 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8257 (ttm110) REVERT: A 825 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8351 (mttp) REVERT: A 900 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: A 957 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: A 994 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: B 237 ARG cc_start: 0.6820 (mmm-85) cc_final: 0.6349 (mtp180) REVERT: B 319 ARG cc_start: 0.8376 (ptp-170) cc_final: 0.8009 (mtt180) REVERT: B 356 LYS cc_start: 0.8217 (tttp) cc_final: 0.7957 (tttt) REVERT: B 357 ARG cc_start: 0.8279 (ttt90) cc_final: 0.7916 (ttt90) REVERT: B 392 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: B 408 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7737 (ttp80) REVERT: B 424 LYS cc_start: 0.7578 (tptt) cc_final: 0.7264 (tppp) REVERT: B 508 TYR cc_start: 0.7833 (m-80) cc_final: 0.7556 (m-80) REVERT: B 556 ASN cc_start: 0.7561 (m-40) cc_final: 0.7184 (p0) REVERT: B 574 ASP cc_start: 0.7980 (t0) cc_final: 0.7698 (t0) REVERT: B 900 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8148 (mtp) REVERT: B 902 MET cc_start: 0.8632 (mmm) cc_final: 0.8376 (mmp) REVERT: B 1092 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: B 1101 HIS cc_start: 0.8113 (m90) cc_final: 0.7844 (m90) REVERT: C 106 PHE cc_start: 0.6203 (m-80) cc_final: 0.5918 (m-80) REVERT: C 356 LYS cc_start: 0.8096 (tttp) cc_final: 0.7859 (tttt) REVERT: C 424 LYS cc_start: 0.7400 (tptp) cc_final: 0.6635 (mttt) REVERT: C 463 PRO cc_start: 0.8796 (Cg_exo) cc_final: 0.8341 (Cg_endo) REVERT: C 529 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8119 (tttp) REVERT: C 582 LEU cc_start: 0.8675 (mt) cc_final: 0.8412 (mt) REVERT: C 586 ASP cc_start: 0.7352 (m-30) cc_final: 0.7085 (m-30) REVERT: C 994 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8173 (m-30) REVERT: C 1092 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7893 (mt-10) outliers start: 70 outliers final: 32 residues processed: 259 average time/residue: 0.4927 time to fit residues: 151.4721 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 55 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 268 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 901 GLN A 955 ASN B 360 ASN C 30 ASN C 314 GLN C 360 ASN C 519 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.188378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124341 restraints weight = 28181.603| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.46 r_work: 0.3354 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24285 Z= 0.123 Angle : 0.572 12.915 33147 Z= 0.288 Chirality : 0.044 0.183 3948 Planarity : 0.004 0.041 4155 Dihedral : 4.862 42.969 4422 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.23 % Allowed : 11.63 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 2844 helix: 1.51 (0.20), residues: 660 sheet: -0.03 (0.20), residues: 579 loop : -0.34 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.023 0.001 TYR B 170 PHE 0.019 0.001 PHE A 464 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00280 (24186) covalent geometry : angle 0.54398 (32886) SS BOND : bond 0.00509 ( 36) SS BOND : angle 1.93443 ( 72) hydrogen bonds : bond 0.03596 ( 1029) hydrogen bonds : angle 5.74576 ( 2814) link_BETA1-4 : bond 0.00300 ( 15) link_BETA1-4 : angle 1.19671 ( 45) link_NAG-ASN : bond 0.00261 ( 48) link_NAG-ASN : angle 2.34979 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7771 (m-80) cc_final: 0.7568 (m-10) REVERT: A 424 LYS cc_start: 0.7786 (tptt) cc_final: 0.6499 (mttp) REVERT: A 464 PHE cc_start: 0.7805 (m-10) cc_final: 0.7591 (m-80) REVERT: A 514 SER cc_start: 0.8618 (t) cc_final: 0.8274 (m) REVERT: A 529 LYS cc_start: 0.8207 (mppt) cc_final: 0.7836 (tmtm) REVERT: A 553 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7159 (p) REVERT: A 558 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7728 (mmtm) REVERT: A 581 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7394 (p) REVERT: A 755 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7546 (mt0) REVERT: A 825 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8272 (mttp) REVERT: A 957 GLN cc_start: 0.8611 (tp40) cc_final: 0.8354 (tt0) REVERT: B 205 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7390 (m) REVERT: B 237 ARG cc_start: 0.6754 (mtm-85) cc_final: 0.6316 (mtp85) REVERT: B 319 ARG cc_start: 0.8389 (ptp-170) cc_final: 0.8017 (mtt180) REVERT: B 356 LYS cc_start: 0.8247 (tttp) cc_final: 0.7987 (tttt) REVERT: B 357 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7837 (ttt90) REVERT: B 392 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: B 408 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7281 (ppt90) REVERT: B 424 LYS cc_start: 0.7544 (tptt) cc_final: 0.7265 (tppp) REVERT: B 508 TYR cc_start: 0.7717 (m-80) cc_final: 0.7484 (m-80) REVERT: B 556 ASN cc_start: 0.7511 (m-40) cc_final: 0.7105 (p0) REVERT: B 574 ASP cc_start: 0.7872 (t0) cc_final: 0.7562 (t0) REVERT: B 900 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8131 (mtp) REVERT: B 902 MET cc_start: 0.8715 (mmm) cc_final: 0.8455 (mmp) REVERT: B 988 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7693 (mt-10) REVERT: B 1092 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: B 1101 HIS cc_start: 0.7941 (m90) cc_final: 0.7655 (m90) REVERT: C 106 PHE cc_start: 0.6088 (m-80) cc_final: 0.5777 (m-80) REVERT: C 205 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7577 (m) REVERT: C 356 LYS cc_start: 0.8146 (tttp) cc_final: 0.7906 (tttt) REVERT: C 359 SER cc_start: 0.8178 (p) cc_final: 0.7814 (t) REVERT: C 360 ASN cc_start: 0.8823 (m-40) cc_final: 0.7799 (t0) REVERT: C 424 LYS cc_start: 0.7356 (tptp) cc_final: 0.6573 (mttt) REVERT: C 463 PRO cc_start: 0.8734 (Cg_exo) cc_final: 0.8251 (Cg_endo) REVERT: C 556 ASN cc_start: 0.8018 (m-40) cc_final: 0.7439 (p0) REVERT: C 574 ASP cc_start: 0.7929 (t0) cc_final: 0.7449 (t0) REVERT: C 582 LEU cc_start: 0.8565 (mt) cc_final: 0.8308 (mm) REVERT: C 586 ASP cc_start: 0.7170 (m-30) cc_final: 0.6826 (m-30) outliers start: 57 outliers final: 21 residues processed: 256 average time/residue: 0.4499 time to fit residues: 138.8594 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 282 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN B 360 ASN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121847 restraints weight = 28254.480| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.37 r_work: 0.3338 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24285 Z= 0.168 Angle : 0.593 14.395 33147 Z= 0.298 Chirality : 0.045 0.176 3948 Planarity : 0.004 0.039 4155 Dihedral : 4.723 41.348 4422 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.19 % Allowed : 12.30 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2844 helix: 1.44 (0.20), residues: 681 sheet: -0.20 (0.19), residues: 603 loop : -0.29 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 408 TYR 0.018 0.001 TYR C 265 PHE 0.021 0.002 PHE B1121 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00399 (24186) covalent geometry : angle 0.56490 (32886) SS BOND : bond 0.00544 ( 36) SS BOND : angle 2.11771 ( 72) hydrogen bonds : bond 0.03755 ( 1029) hydrogen bonds : angle 5.75557 ( 2814) link_BETA1-4 : bond 0.00277 ( 15) link_BETA1-4 : angle 1.21986 ( 45) link_NAG-ASN : bond 0.00255 ( 48) link_NAG-ASN : angle 2.30438 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7483 (ttp80) REVERT: A 356 LYS cc_start: 0.8072 (tttp) cc_final: 0.7717 (tttt) REVERT: A 424 LYS cc_start: 0.7825 (tptt) cc_final: 0.6492 (mttp) REVERT: A 514 SER cc_start: 0.8648 (t) cc_final: 0.8072 (m) REVERT: A 529 LYS cc_start: 0.8236 (mppt) cc_final: 0.7979 (mppt) REVERT: A 553 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7233 (p) REVERT: A 558 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7819 (mmtm) REVERT: A 646 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7966 (ttp-170) REVERT: A 825 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8280 (mttp) REVERT: A 900 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: A 957 GLN cc_start: 0.8661 (tp40) cc_final: 0.8431 (tt0) REVERT: A 994 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: B 205 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7423 (m) REVERT: B 237 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6322 (mtp85) REVERT: B 319 ARG cc_start: 0.8373 (ptp-170) cc_final: 0.7979 (mtt180) REVERT: B 356 LYS cc_start: 0.8258 (tttp) cc_final: 0.7989 (tttt) REVERT: B 357 ARG cc_start: 0.8239 (ttt90) cc_final: 0.7843 (ttt90) REVERT: B 392 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6539 (m-80) REVERT: B 408 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7771 (ttp80) REVERT: B 424 LYS cc_start: 0.7535 (tptt) cc_final: 0.7239 (tppp) REVERT: B 508 TYR cc_start: 0.7785 (m-80) cc_final: 0.7533 (m-80) REVERT: B 556 ASN cc_start: 0.7576 (m-40) cc_final: 0.7252 (p0) REVERT: B 574 ASP cc_start: 0.7923 (t0) cc_final: 0.7618 (t0) REVERT: B 900 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8195 (mtp) REVERT: B 902 MET cc_start: 0.8707 (mmm) cc_final: 0.8494 (mmp) REVERT: B 988 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 1092 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: B 1101 HIS cc_start: 0.7956 (m90) cc_final: 0.7632 (m90) REVERT: C 106 PHE cc_start: 0.6186 (m-80) cc_final: 0.5968 (m-80) REVERT: C 190 ARG cc_start: 0.7102 (ttp-170) cc_final: 0.6782 (ttp80) REVERT: C 356 LYS cc_start: 0.8151 (tttp) cc_final: 0.7903 (tttt) REVERT: C 359 SER cc_start: 0.8227 (p) cc_final: 0.7865 (t) REVERT: C 360 ASN cc_start: 0.8692 (m-40) cc_final: 0.8274 (m-40) REVERT: C 424 LYS cc_start: 0.7369 (tptp) cc_final: 0.6596 (mttt) REVERT: C 463 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8160 (Cg_endo) REVERT: C 556 ASN cc_start: 0.8031 (m-40) cc_final: 0.7461 (p0) REVERT: C 574 ASP cc_start: 0.8001 (t0) cc_final: 0.7471 (t0) REVERT: C 582 LEU cc_start: 0.8572 (mt) cc_final: 0.8328 (mm) REVERT: C 586 ASP cc_start: 0.7239 (m-30) cc_final: 0.6861 (m-30) REVERT: C 592 PHE cc_start: 0.7530 (p90) cc_final: 0.7278 (p90) REVERT: C 790 LYS cc_start: 0.8730 (pttt) cc_final: 0.8371 (pttp) REVERT: C 994 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8163 (m-30) outliers start: 56 outliers final: 26 residues processed: 251 average time/residue: 0.4873 time to fit residues: 144.8599 Evaluate side-chains 230 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 137 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 901 GLN B 360 ASN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.183893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119139 restraints weight = 28037.380| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.33 r_work: 0.3311 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24285 Z= 0.199 Angle : 0.608 14.486 33147 Z= 0.305 Chirality : 0.046 0.170 3948 Planarity : 0.004 0.040 4155 Dihedral : 4.736 41.185 4422 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.43 % Allowed : 12.77 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 2844 helix: 1.35 (0.20), residues: 675 sheet: -0.16 (0.19), residues: 591 loop : -0.44 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.023 0.002 TYR B 170 PHE 0.022 0.002 PHE B1121 TRP 0.009 0.002 TRP B1102 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00478 (24186) covalent geometry : angle 0.58022 (32886) SS BOND : bond 0.00564 ( 36) SS BOND : angle 2.18180 ( 72) hydrogen bonds : bond 0.03831 ( 1029) hydrogen bonds : angle 5.81967 ( 2814) link_BETA1-4 : bond 0.00229 ( 15) link_BETA1-4 : angle 1.25627 ( 45) link_NAG-ASN : bond 0.00296 ( 48) link_NAG-ASN : angle 2.28488 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7448 (ttp80) REVERT: A 424 LYS cc_start: 0.7698 (tptt) cc_final: 0.6459 (mtmt) REVERT: A 514 SER cc_start: 0.8610 (t) cc_final: 0.8006 (m) REVERT: A 529 LYS cc_start: 0.8282 (mppt) cc_final: 0.7952 (mppt) REVERT: A 553 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7099 (p) REVERT: A 558 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7817 (mmtm) REVERT: A 581 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7382 (p) REVERT: A 646 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7977 (ttp-170) REVERT: A 825 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8184 (mttp) REVERT: A 900 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8453 (mtp) REVERT: A 947 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7798 (mtmm) REVERT: A 957 GLN cc_start: 0.8599 (tp40) cc_final: 0.8365 (tt0) REVERT: A 994 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: B 205 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7355 (m) REVERT: B 237 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.6242 (mtp180) REVERT: B 319 ARG cc_start: 0.8276 (ptp-170) cc_final: 0.7886 (mtt180) REVERT: B 356 LYS cc_start: 0.8116 (tttp) cc_final: 0.7838 (tttt) REVERT: B 408 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7748 (ttp80) REVERT: B 424 LYS cc_start: 0.7484 (tptt) cc_final: 0.7189 (tppp) REVERT: B 508 TYR cc_start: 0.7687 (m-80) cc_final: 0.7427 (m-80) REVERT: B 556 ASN cc_start: 0.7628 (m-40) cc_final: 0.7227 (p0) REVERT: B 574 ASP cc_start: 0.7858 (t0) cc_final: 0.7521 (t0) REVERT: B 900 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: B 988 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 1092 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: B 1101 HIS cc_start: 0.7910 (m90) cc_final: 0.7559 (m90) REVERT: C 118 LEU cc_start: 0.6573 (tt) cc_final: 0.6338 (tm) REVERT: C 190 ARG cc_start: 0.7132 (ttp-170) cc_final: 0.6798 (ttp80) REVERT: C 356 LYS cc_start: 0.8056 (tttp) cc_final: 0.7801 (tttt) REVERT: C 359 SER cc_start: 0.8187 (p) cc_final: 0.7807 (t) REVERT: C 360 ASN cc_start: 0.8658 (m-40) cc_final: 0.8249 (m-40) REVERT: C 463 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8359 (Cg_endo) REVERT: C 529 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7618 (mppt) REVERT: C 556 ASN cc_start: 0.8037 (m-40) cc_final: 0.7364 (p0) REVERT: C 574 ASP cc_start: 0.7959 (t0) cc_final: 0.7410 (t0) REVERT: C 582 LEU cc_start: 0.8528 (mt) cc_final: 0.8296 (mm) REVERT: C 586 ASP cc_start: 0.7184 (m-30) cc_final: 0.6787 (m-30) REVERT: C 994 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: C 1138 TYR cc_start: 0.7528 (t80) cc_final: 0.7318 (t80) outliers start: 62 outliers final: 31 residues processed: 236 average time/residue: 0.4948 time to fit residues: 139.0627 Evaluate side-chains 226 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 9.9990 chunk 274 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 290 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN B 360 ASN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.182934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118941 restraints weight = 28065.104| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.32 r_work: 0.3400 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 24285 Z= 0.231 Angle : 0.633 14.693 33147 Z= 0.318 Chirality : 0.046 0.176 3948 Planarity : 0.004 0.038 4155 Dihedral : 4.864 41.721 4422 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.27 % Allowed : 13.28 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 2844 helix: 1.22 (0.20), residues: 678 sheet: -0.24 (0.19), residues: 591 loop : -0.52 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 408 TYR 0.021 0.002 TYR B 170 PHE 0.024 0.002 PHE B 238 TRP 0.011 0.002 TRP B1102 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00555 (24186) covalent geometry : angle 0.60742 (32886) SS BOND : bond 0.00603 ( 36) SS BOND : angle 2.20458 ( 72) hydrogen bonds : bond 0.03981 ( 1029) hydrogen bonds : angle 5.91372 ( 2814) link_BETA1-4 : bond 0.00254 ( 15) link_BETA1-4 : angle 1.27641 ( 45) link_NAG-ASN : bond 0.00314 ( 48) link_NAG-ASN : angle 2.26730 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7473 (ttp80) REVERT: A 424 LYS cc_start: 0.7788 (tptt) cc_final: 0.6520 (mttt) REVERT: A 514 SER cc_start: 0.8714 (t) cc_final: 0.8160 (m) REVERT: A 529 LYS cc_start: 0.8292 (mppt) cc_final: 0.7978 (mppt) REVERT: A 553 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7184 (p) REVERT: A 581 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7411 (p) REVERT: A 646 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8010 (ttp-170) REVERT: A 825 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8211 (mttp) REVERT: A 900 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8482 (mtp) REVERT: A 947 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7820 (mtmm) REVERT: A 957 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: A 994 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: B 205 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7431 (m) REVERT: B 237 ARG cc_start: 0.6736 (mtm-85) cc_final: 0.6299 (mtp180) REVERT: B 319 ARG cc_start: 0.8296 (ptp-170) cc_final: 0.7906 (mtt180) REVERT: B 356 LYS cc_start: 0.8218 (tttp) cc_final: 0.7954 (tttt) REVERT: B 408 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7807 (ttp80) REVERT: B 424 LYS cc_start: 0.7478 (tptt) cc_final: 0.7218 (tppp) REVERT: B 508 TYR cc_start: 0.7728 (m-80) cc_final: 0.7482 (m-80) REVERT: B 556 ASN cc_start: 0.7617 (m-40) cc_final: 0.7218 (p0) REVERT: B 574 ASP cc_start: 0.7948 (t0) cc_final: 0.7638 (t0) REVERT: B 661 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8102 (mm-30) REVERT: B 825 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7988 (mttt) REVERT: B 900 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8139 (mtp) REVERT: B 988 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 1092 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: B 1101 HIS cc_start: 0.7969 (m90) cc_final: 0.7613 (m90) REVERT: C 190 ARG cc_start: 0.7198 (ttp-170) cc_final: 0.6872 (ttp80) REVERT: C 356 LYS cc_start: 0.8100 (tttp) cc_final: 0.7834 (tttt) REVERT: C 359 SER cc_start: 0.8234 (p) cc_final: 0.7894 (t) REVERT: C 360 ASN cc_start: 0.8679 (m-40) cc_final: 0.8278 (m-40) REVERT: C 424 LYS cc_start: 0.7519 (tptp) cc_final: 0.6586 (mptt) REVERT: C 463 PRO cc_start: 0.8665 (Cg_exo) cc_final: 0.8276 (Cg_endo) REVERT: C 529 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7702 (mppt) REVERT: C 556 ASN cc_start: 0.8021 (m-40) cc_final: 0.7366 (p0) REVERT: C 574 ASP cc_start: 0.7956 (t0) cc_final: 0.7396 (t0) REVERT: C 582 LEU cc_start: 0.8576 (mt) cc_final: 0.8355 (mm) REVERT: C 586 ASP cc_start: 0.7219 (m-30) cc_final: 0.6877 (m-30) REVERT: C 760 CYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6059 (t) REVERT: C 994 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8141 (m-30) outliers start: 58 outliers final: 30 residues processed: 237 average time/residue: 0.5037 time to fit residues: 140.6136 Evaluate side-chains 227 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 170 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 188 ASN B 360 ASN B 519 HIS C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.187857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126162 restraints weight = 28803.981| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.27 r_work: 0.3418 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24285 Z= 0.151 Angle : 0.572 14.639 33147 Z= 0.288 Chirality : 0.044 0.166 3948 Planarity : 0.004 0.040 4155 Dihedral : 4.575 41.681 4422 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.96 % Allowed : 14.06 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 2844 helix: 1.43 (0.20), residues: 687 sheet: -0.26 (0.20), residues: 573 loop : -0.39 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.024 0.001 TYR B 170 PHE 0.022 0.001 PHE B 238 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00356 (24186) covalent geometry : angle 0.54864 (32886) SS BOND : bond 0.00525 ( 36) SS BOND : angle 1.96089 ( 72) hydrogen bonds : bond 0.03589 ( 1029) hydrogen bonds : angle 5.66877 ( 2814) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 1.11280 ( 45) link_NAG-ASN : bond 0.00214 ( 48) link_NAG-ASN : angle 2.06816 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7303 (ttp80) REVERT: A 424 LYS cc_start: 0.7805 (tptt) cc_final: 0.6528 (mttp) REVERT: A 514 SER cc_start: 0.8661 (t) cc_final: 0.8351 (m) REVERT: A 529 LYS cc_start: 0.8298 (mppt) cc_final: 0.7994 (mppt) REVERT: A 553 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7222 (p) REVERT: A 556 ASN cc_start: 0.8075 (m-40) cc_final: 0.7462 (m110) REVERT: A 558 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7604 (mmtm) REVERT: A 581 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 646 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7984 (ttp-170) REVERT: A 825 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8224 (mttp) REVERT: A 900 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8447 (mtp) REVERT: A 957 GLN cc_start: 0.8658 (tp40) cc_final: 0.8431 (tt0) REVERT: A 994 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: B 205 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7471 (m) REVERT: B 237 ARG cc_start: 0.6750 (mtm-85) cc_final: 0.6310 (mtp180) REVERT: B 319 ARG cc_start: 0.8302 (ptp-170) cc_final: 0.7917 (mtt180) REVERT: B 356 LYS cc_start: 0.8286 (tttp) cc_final: 0.8014 (tttt) REVERT: B 408 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7269 (ppt90) REVERT: B 424 LYS cc_start: 0.7554 (tptt) cc_final: 0.7278 (tppp) REVERT: B 556 ASN cc_start: 0.7558 (m-40) cc_final: 0.7207 (p0) REVERT: B 574 ASP cc_start: 0.7929 (t0) cc_final: 0.7634 (t0) REVERT: B 825 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8074 (mttt) REVERT: B 900 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8167 (mtp) REVERT: B 988 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7799 (mt-10) REVERT: B 1092 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: B 1101 HIS cc_start: 0.7898 (m90) cc_final: 0.7592 (m90) REVERT: C 118 LEU cc_start: 0.6714 (tt) cc_final: 0.6469 (tm) REVERT: C 190 ARG cc_start: 0.7213 (ttp-170) cc_final: 0.6896 (ttp80) REVERT: C 239 GLN cc_start: 0.6735 (mt0) cc_final: 0.6125 (mm-40) REVERT: C 356 LYS cc_start: 0.8180 (tttp) cc_final: 0.7875 (tttt) REVERT: C 359 SER cc_start: 0.8254 (p) cc_final: 0.7942 (t) REVERT: C 360 ASN cc_start: 0.8708 (m-40) cc_final: 0.8305 (m-40) REVERT: C 424 LYS cc_start: 0.7471 (tptp) cc_final: 0.6583 (mttt) REVERT: C 463 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8323 (Cg_endo) REVERT: C 529 LYS cc_start: 0.8413 (tttp) cc_final: 0.7677 (mppt) REVERT: C 556 ASN cc_start: 0.8018 (m-40) cc_final: 0.7355 (p0) REVERT: C 574 ASP cc_start: 0.7913 (t0) cc_final: 0.7386 (t0) REVERT: C 586 ASP cc_start: 0.7299 (m-30) cc_final: 0.6893 (m-30) REVERT: C 760 CYS cc_start: 0.6810 (OUTLIER) cc_final: 0.5909 (t) REVERT: C 790 LYS cc_start: 0.8746 (pttt) cc_final: 0.8363 (pttp) REVERT: C 994 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8148 (m-30) outliers start: 50 outliers final: 29 residues processed: 234 average time/residue: 0.4959 time to fit residues: 137.8152 Evaluate side-chains 226 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 0.8980 chunk 273 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 287 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN B 519 HIS C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.183151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118748 restraints weight = 28112.296| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.22 r_work: 0.3409 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 24285 Z= 0.230 Angle : 0.633 14.655 33147 Z= 0.319 Chirality : 0.046 0.213 3948 Planarity : 0.004 0.041 4155 Dihedral : 4.725 41.452 4422 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.04 % Allowed : 13.87 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 2844 helix: 1.21 (0.20), residues: 681 sheet: -0.28 (0.19), residues: 591 loop : -0.51 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 408 TYR 0.035 0.002 TYR B 508 PHE 0.023 0.002 PHE B 238 TRP 0.010 0.002 TRP B1102 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00553 (24186) covalent geometry : angle 0.60622 (32886) SS BOND : bond 0.00632 ( 36) SS BOND : angle 2.48740 ( 72) hydrogen bonds : bond 0.03920 ( 1029) hydrogen bonds : angle 5.86067 ( 2814) link_BETA1-4 : bond 0.00242 ( 15) link_BETA1-4 : angle 1.23760 ( 45) link_NAG-ASN : bond 0.00301 ( 48) link_NAG-ASN : angle 2.16558 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7297 (ttp80) REVERT: A 424 LYS cc_start: 0.7782 (tptt) cc_final: 0.6504 (mttp) REVERT: A 514 SER cc_start: 0.8678 (t) cc_final: 0.8129 (m) REVERT: A 529 LYS cc_start: 0.8299 (mppt) cc_final: 0.8018 (mppt) REVERT: A 553 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7209 (p) REVERT: A 558 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7560 (mmtm) REVERT: A 581 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7409 (p) REVERT: A 646 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7986 (ttp-170) REVERT: A 825 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8212 (mttp) REVERT: A 900 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: A 957 GLN cc_start: 0.8616 (tp40) cc_final: 0.8391 (tt0) REVERT: A 994 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: B 205 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7415 (m) REVERT: B 237 ARG cc_start: 0.6716 (mtm-85) cc_final: 0.6282 (mtp180) REVERT: B 319 ARG cc_start: 0.8303 (ptp-170) cc_final: 0.7912 (mtt180) REVERT: B 356 LYS cc_start: 0.8262 (tttp) cc_final: 0.7994 (tttt) REVERT: B 408 ARG cc_start: 0.8002 (ttp-110) cc_final: 0.7799 (ttp80) REVERT: B 424 LYS cc_start: 0.7453 (tptt) cc_final: 0.7179 (tppp) REVERT: B 465 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.4145 (pm20) REVERT: B 508 TYR cc_start: 0.7575 (m-80) cc_final: 0.7295 (m-80) REVERT: B 556 ASN cc_start: 0.7661 (m-40) cc_final: 0.7259 (p0) REVERT: B 574 ASP cc_start: 0.7962 (t0) cc_final: 0.7640 (t0) REVERT: B 661 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8092 (mm-30) REVERT: B 825 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8061 (mttt) REVERT: B 900 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8206 (mtp) REVERT: B 988 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 1092 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: B 1101 HIS cc_start: 0.7902 (m90) cc_final: 0.7562 (m90) REVERT: C 118 LEU cc_start: 0.6588 (tt) cc_final: 0.6332 (tm) REVERT: C 190 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6924 (ttp80) REVERT: C 271 GLN cc_start: 0.7758 (mt0) cc_final: 0.7511 (mp10) REVERT: C 356 LYS cc_start: 0.8183 (tttp) cc_final: 0.7866 (tttt) REVERT: C 359 SER cc_start: 0.8254 (p) cc_final: 0.7914 (t) REVERT: C 360 ASN cc_start: 0.8687 (m-40) cc_final: 0.8228 (m-40) REVERT: C 424 LYS cc_start: 0.7546 (tptp) cc_final: 0.6573 (mttt) REVERT: C 463 PRO cc_start: 0.8617 (Cg_exo) cc_final: 0.8301 (Cg_endo) REVERT: C 529 LYS cc_start: 0.8429 (tttp) cc_final: 0.7750 (mppt) REVERT: C 556 ASN cc_start: 0.8037 (m-40) cc_final: 0.7371 (p0) REVERT: C 574 ASP cc_start: 0.7912 (t0) cc_final: 0.7354 (t0) REVERT: C 586 ASP cc_start: 0.7187 (m-30) cc_final: 0.6833 (m-30) REVERT: C 592 PHE cc_start: 0.7523 (p90) cc_final: 0.7289 (p90) REVERT: C 994 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8139 (m-30) outliers start: 52 outliers final: 29 residues processed: 227 average time/residue: 0.5084 time to fit residues: 137.0136 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 218 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 901 GLN B 360 ASN B 519 HIS C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.187684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124921 restraints weight = 28724.193| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.20 r_work: 0.3328 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 24285 Z= 0.167 Angle : 0.599 14.584 33147 Z= 0.301 Chirality : 0.045 0.189 3948 Planarity : 0.004 0.040 4155 Dihedral : 4.586 41.215 4422 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 14.18 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 2844 helix: 1.36 (0.20), residues: 678 sheet: -0.33 (0.20), residues: 573 loop : -0.43 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.024 0.001 TYR B 508 PHE 0.023 0.001 PHE B 238 TRP 0.010 0.001 TRP A 353 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00396 (24186) covalent geometry : angle 0.56872 (32886) SS BOND : bond 0.00491 ( 36) SS BOND : angle 2.81942 ( 72) hydrogen bonds : bond 0.03675 ( 1029) hydrogen bonds : angle 5.77200 ( 2814) link_BETA1-4 : bond 0.00324 ( 15) link_BETA1-4 : angle 1.15341 ( 45) link_NAG-ASN : bond 0.00222 ( 48) link_NAG-ASN : angle 2.06979 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8818.51 seconds wall clock time: 150 minutes 34.25 seconds (9034.25 seconds total)