Starting phenix.real_space_refine on Sat Jul 4 21:49:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kdk_22825/07_2026/7kdk_22825.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdk_22825/07_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_22825/07_2026/7kdk_22825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdk_22825/07_2026/7kdk_22825.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kdk_22825/07_2026/7kdk_22825.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kdk_22825/07_2026/7kdk_22825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kdk_22825/07_2026/7kdk_22825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdk_22825/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 4.35, per 1000 atoms: 0.18 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.69 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: 4.97 Time building geometry restraints manager: 2.41 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: 12905 17.94 - 35.87: 795 35.87 - 53.81: 113 53.81 - 71.75: 48 71.75 - 89.68: 29 Dihedral angle restraints: 13890 sinusoidal: 5406 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 13887 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: 0.03 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: 1.760 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.510 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 13.026 89.682 8304 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/Z covalent geometry : bond 0.01394 / 0.79 (24186) covalent geometry : angle 1.78418 / 1.19 (32886) SS BOND : bond 0.01890 / 1.04 ( 36) SS BOND : angle 2.52929 / 1.73 ( 72) hydrogen bonds : bond 0.14022 / 8.89 ( 1029) hydrogen bonds : angle 8.14526 / 5.61 ( 2814) link_BETA1-4 : bond 0.02586 / 1.49 ( 15) link_BETA1-4 : angle 4.68550 / 2.99 ( 45) link_NAG-ASN : bond 0.01237 / 0.81 ( 48) link_NAG-ASN : angle 4.46634 / 3.00 ( 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 : 0.732 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: 0.5231 time to fit residues: 244.0191 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 : 0.879 ------------------------------------------------------------------------------- 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... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 314 GLN B 321 GLN B 360 ASN B 394 ASN B 675 GLN 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 = 0.4340 r_free = 0.4340 target = 0.190805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124044 restraints weight = 28509.728| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.14 r_work: 0.3524 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 24285 Z= 0.169 Angle : 0.790 27.947 33147 Z= 0.385 Chirality : 0.048 0.294 3948 Planarity : 0.004 0.040 4155 Dihedral : 5.890 30.965 3103 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 7.79 % Favored : 90.05 % 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: 1.19 (0.20), residues: 639 sheet: -0.04 (0.19), residues: 615 loop : -0.52 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.032 0.002 TYR A 508 PHE 0.021 0.002 PHE B 58 TRP 0.015 0.002 TRP A 64 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (24186) covalent geometry : angle 0.71001 / 0.37 (32886) SS BOND : bond 0.00744 / 0.42 ( 36) SS BOND : angle 2.98407 / 1.78 ( 72) hydrogen bonds : bond 0.04464 / 2.90 ( 1029) hydrogen bonds : angle 6.41906 / 4.43 ( 2814) link_BETA1-4 : bond 0.00406 / 0.24 ( 15) link_BETA1-4 : angle 1.68619 / 1.08 ( 45) link_NAG-ASN : bond 0.00339 / 0.21 ( 48) link_NAG-ASN : angle 4.79898 / 3.06 ( 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: 55 poor density : 253 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 357 ARG cc_start: 0.8183 (ttt-90) cc_final: 0.7471 (mmm160) REVERT: A 394 ASN cc_start: 0.7838 (m-40) cc_final: 0.7334 (m-40) REVERT: A 424 LYS cc_start: 0.7799 (tptt) cc_final: 0.6570 (mttt) REVERT: A 529 LYS cc_start: 0.8287 (mppt) cc_final: 0.7921 (tmtm) REVERT: A 532 ASN cc_start: 0.8500 (t0) cc_final: 0.8201 (t0) REVERT: A 957 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 988 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 237 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.6143 (mtp180) REVERT: B 319 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.7453 (ptm160) REVERT: B 356 LYS cc_start: 0.8205 (tttp) cc_final: 0.7995 (tttt) REVERT: B 424 LYS cc_start: 0.7645 (tptt) cc_final: 0.7302 (tppp) REVERT: B 556 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7088 (p0) REVERT: B 663 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8496 (t0) REVERT: B 740 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8403 (ttp) REVERT: B 900 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: B 988 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7531 (mt-10) REVERT: B 1092 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: B 1101 HIS cc_start: 0.7978 (m90) cc_final: 0.7646 (m90) REVERT: C 128 ILE cc_start: 0.6440 (mt) cc_final: 0.5932 (mp) REVERT: C 356 LYS cc_start: 0.8088 (tttp) cc_final: 0.7851 (tttt) REVERT: C 400 PHE cc_start: 0.8227 (p90) cc_final: 0.8023 (p90) REVERT: C 424 LYS cc_start: 0.7333 (tptp) cc_final: 0.6670 (mttt) REVERT: C 463 PRO cc_start: 0.8802 (Cg_exo) cc_final: 0.8302 (Cg_endo) REVERT: C 556 ASN cc_start: 0.7868 (m-40) cc_final: 0.7409 (p0) REVERT: C 582 LEU cc_start: 0.8577 (mt) cc_final: 0.8357 (mm) REVERT: C 586 ASP cc_start: 0.7368 (m-30) cc_final: 0.7064 (m-30) REVERT: C 964 LYS cc_start: 0.8692 (mttt) cc_final: 0.8282 (mmmt) REVERT: C 1091 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7728 (mtt-85) outliers start: 55 outliers final: 23 residues processed: 289 average time/residue: 0.4480 time to fit residues: 153.7122 Evaluate side-chains 224 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 735 SER 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 422 ASN 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 588 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET 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 172 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS 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 750 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: 0.9980 chunk 10 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 519 HIS A 675 GLN A1010 GLN B 207 HIS B 334 ASN B 360 ASN B 564 GLN B1010 GLN C 314 GLN C 360 ASN C 394 ASN C 519 HIS C1010 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.190374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124051 restraints weight = 28654.301| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.13 r_work: 0.3517 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24285 Z= 0.151 Angle : 0.637 11.894 33147 Z= 0.322 Chirality : 0.046 0.258 3948 Planarity : 0.004 0.039 4155 Dihedral : 5.205 23.546 3099 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.43 % Allowed : 9.24 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.15), residues: 2844 helix: 1.43 (0.20), residues: 642 sheet: 0.21 (0.19), residues: 567 loop : -0.44 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 190 TYR 0.034 0.002 TYR A 396 PHE 0.019 0.002 PHE B1121 TRP 0.011 0.002 TRP A 64 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (24186) covalent geometry : angle 0.60391 / 0.31 (32886) SS BOND : bond 0.00666 / 0.44 ( 36) SS BOND : angle 2.37159 / 1.40 ( 72) hydrogen bonds : bond 0.04001 / 2.61 ( 1029) hydrogen bonds : angle 5.98498 / 4.13 ( 2814) link_BETA1-4 : bond 0.00333 / 0.19 ( 15) link_BETA1-4 : angle 1.32924 / 0.88 ( 45) link_NAG-ASN : bond 0.00291 / 0.21 ( 48) link_NAG-ASN : angle 2.59076 / 1.71 ( 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 283 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7826 (m-80) cc_final: 0.7618 (m-10) REVERT: A 190 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7057 (ttp80) REVERT: A 326 ILE cc_start: 0.7273 (mm) cc_final: 0.6986 (tt) REVERT: A 357 ARG cc_start: 0.8399 (ttt-90) cc_final: 0.7925 (tpt-90) REVERT: A 392 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: A 424 LYS cc_start: 0.7739 (tptt) cc_final: 0.6398 (mttp) REVERT: A 529 LYS cc_start: 0.8186 (mppt) cc_final: 0.7759 (tttp) REVERT: A 532 ASN cc_start: 0.8501 (t0) cc_final: 0.8202 (t0) REVERT: A 553 THR cc_start: 0.7702 (m) cc_final: 0.7344 (p) REVERT: A 586 ASP cc_start: 0.6863 (t0) cc_final: 0.6612 (t0) REVERT: A 825 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8302 (mttp) REVERT: A 957 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: A 994 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: B 190 ARG cc_start: 0.7451 (mtp180) cc_final: 0.7196 (mtp180) REVERT: B 205 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7180 (m) REVERT: B 226 LEU cc_start: 0.6312 (mt) cc_final: 0.6055 (mt) REVERT: B 237 ARG cc_start: 0.6753 (mmm-85) cc_final: 0.6277 (mtp180) REVERT: B 319 ARG cc_start: 0.8386 (ptp-170) cc_final: 0.7997 (mtt180) REVERT: B 356 LYS cc_start: 0.8148 (tttp) cc_final: 0.7903 (tttt) REVERT: B 357 ARG cc_start: 0.8064 (ttt90) cc_final: 0.7660 (ttt90) REVERT: B 424 LYS cc_start: 0.7566 (tptt) cc_final: 0.7306 (tppp) REVERT: B 508 TYR cc_start: 0.7836 (m-80) cc_final: 0.7539 (m-80) REVERT: B 556 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7106 (p0) REVERT: B 900 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8173 (mtp) REVERT: B 988 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 1092 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: C 205 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7707 (m) REVERT: C 356 LYS cc_start: 0.8181 (tttp) cc_final: 0.7975 (tttt) REVERT: C 400 PHE cc_start: 0.8254 (p90) cc_final: 0.7992 (p90) REVERT: C 424 LYS cc_start: 0.7384 (tptp) cc_final: 0.6660 (mttt) REVERT: C 463 PRO cc_start: 0.8792 (Cg_exo) cc_final: 0.8285 (Cg_endo) REVERT: C 556 ASN cc_start: 0.7849 (m-40) cc_final: 0.7384 (p0) REVERT: C 582 LEU cc_start: 0.8681 (mt) cc_final: 0.8458 (mm) REVERT: C 586 ASP cc_start: 0.7241 (m-30) cc_final: 0.6948 (m-30) REVERT: C 964 LYS cc_start: 0.8721 (mttt) cc_final: 0.8360 (mmmt) REVERT: C 985 ASP cc_start: 0.7859 (p0) cc_final: 0.7654 (p0) outliers start: 62 outliers final: 21 residues processed: 261 average time/residue: 0.5223 time to fit residues: 161.3714 Evaluate side-chains 217 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 608 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR 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 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 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 392 PHE 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: 0.4980 chunk 28 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 360 ASN A 394 ASN A 675 GLN B 334 ASN B 360 ASN B 564 GLN C 314 GLN C 360 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.189360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123564 restraints weight = 28410.238| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.12 r_work: 0.3382 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24285 Z= 0.167 Angle : 0.610 14.611 33147 Z= 0.308 Chirality : 0.045 0.294 3948 Planarity : 0.004 0.042 4155 Dihedral : 4.926 21.419 3099 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.43 % Allowed : 10.58 % Favored : 87.00 % 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: 0.28 (0.15), residues: 2844 helix: 1.55 (0.21), residues: 639 sheet: 0.24 (0.20), residues: 570 loop : -0.35 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.022 0.002 TYR B 170 PHE 0.020 0.002 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (24186) covalent geometry : angle 0.58315 / 0.30 (32886) SS BOND : bond 0.00519 / 0.33 ( 36) SS BOND : angle 2.31864 / 1.35 ( 72) hydrogen bonds : bond 0.03881 / 2.52 ( 1029) hydrogen bonds : angle 5.88227 / 4.06 ( 2814) link_BETA1-4 : bond 0.00330 / 0.18 ( 15) link_BETA1-4 : angle 1.20473 / 0.80 ( 45) link_NAG-ASN : bond 0.00255 / 0.16 ( 48) link_NAG-ASN : angle 2.18696 / 1.43 ( 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 265 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 0.727 Fit side-chains REVERT: A 357 ARG cc_start: 0.8319 (ttt-90) cc_final: 0.7877 (tpt-90) REVERT: A 367 VAL cc_start: 0.9101 (t) cc_final: 0.8839 (m) REVERT: A 424 LYS cc_start: 0.7595 (tptt) cc_final: 0.6383 (mttp) REVERT: A 529 LYS cc_start: 0.8227 (mppt) cc_final: 0.7783 (tttp) REVERT: A 553 THR cc_start: 0.7535 (m) cc_final: 0.7104 (p) REVERT: A 646 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8212 (ttm110) REVERT: A 755 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7505 (mt0) REVERT: A 825 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8264 (mttp) REVERT: A 957 GLN cc_start: 0.8553 (tp40) cc_final: 0.8304 (tt0) REVERT: A 994 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8208 (m-30) REVERT: B 205 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7189 (m) REVERT: B 226 LEU cc_start: 0.6129 (mt) cc_final: 0.5728 (mt) REVERT: B 237 ARG cc_start: 0.6691 (mtm-85) cc_final: 0.6235 (mtp180) REVERT: B 271 GLN cc_start: 0.7757 (mt0) cc_final: 0.7521 (mp10) REVERT: B 356 LYS cc_start: 0.8156 (tttp) cc_final: 0.7890 (tttt) REVERT: B 357 ARG cc_start: 0.8092 (ttt90) cc_final: 0.7681 (ttt90) REVERT: B 392 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6624 (m-80) REVERT: B 408 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7678 (ttp80) REVERT: B 424 LYS cc_start: 0.7520 (tptt) cc_final: 0.7208 (tppp) REVERT: B 508 TYR cc_start: 0.7780 (m-80) cc_final: 0.7514 (m-80) REVERT: B 556 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7137 (p0) REVERT: B 574 ASP cc_start: 0.7801 (t0) cc_final: 0.7516 (t0) REVERT: B 661 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8111 (mm-30) REVERT: B 663 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8543 (t0) REVERT: B 900 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8149 (mtp) REVERT: B 988 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7637 (mt-10) REVERT: B 1092 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: C 106 PHE cc_start: 0.6028 (m-80) cc_final: 0.5692 (m-80) REVERT: C 356 LYS cc_start: 0.8106 (tttp) cc_final: 0.7864 (tttt) REVERT: C 424 LYS cc_start: 0.7327 (tptp) cc_final: 0.6587 (mttt) REVERT: C 463 PRO cc_start: 0.8792 (Cg_exo) cc_final: 0.8382 (Cg_endo) REVERT: C 556 ASN cc_start: 0.7908 (m-40) cc_final: 0.7381 (p0) REVERT: C 582 LEU cc_start: 0.8593 (mt) cc_final: 0.8353 (mm) REVERT: C 586 ASP cc_start: 0.7032 (m-30) cc_final: 0.6757 (m-30) REVERT: C 964 LYS cc_start: 0.8735 (mttt) cc_final: 0.8292 (mmmt) REVERT: C 994 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8189 (m-30) outliers start: 62 outliers final: 27 residues processed: 250 average time/residue: 0.4739 time to fit residues: 140.8615 Evaluate side-chains 220 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 SER 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 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 205 SER 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 392 PHE Chi-restraints excluded: chain B residue 393 THR 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 820 ASP 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 205 SER 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 615 VAL 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 900 MET Chi-restraints excluded: chain C residue 994 ASP 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: 2.9990 chunk 165 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 163 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 901 GLN B 360 ASN C 30 ASN C 314 GLN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.188590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125499 restraints weight = 28128.692| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.67 r_work: 0.3345 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24285 Z= 0.134 Angle : 0.573 12.533 33147 Z= 0.289 Chirality : 0.044 0.263 3948 Planarity : 0.003 0.040 4155 Dihedral : 4.718 21.895 3099 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.19 % Allowed : 11.32 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.29 (0.15), residues: 2844 helix: 1.55 (0.21), residues: 657 sheet: 0.07 (0.20), residues: 579 loop : -0.28 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.023 0.001 TYR B 170 PHE 0.017 0.001 PHE A 318 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (24186) covalent geometry : angle 0.54871 / 0.28 (32886) SS BOND : bond 0.00530 / 0.33 ( 36) SS BOND : angle 1.98746 / 1.20 ( 72) hydrogen bonds : bond 0.03624 / 2.37 ( 1029) hydrogen bonds : angle 5.71102 / 3.94 ( 2814) link_BETA1-4 : bond 0.00290 / 0.17 ( 15) link_BETA1-4 : angle 1.10603 / 0.73 ( 45) link_NAG-ASN : bond 0.00254 / 0.16 ( 48) link_NAG-ASN : angle 2.11244 / 1.39 ( 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 255 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 0.757 Fit side-chains REVERT: A 190 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7473 (ttp80) REVERT: A 357 ARG cc_start: 0.8264 (ttt-90) cc_final: 0.7891 (tpt-90) REVERT: A 367 VAL cc_start: 0.9078 (t) cc_final: 0.8871 (m) REVERT: A 424 LYS cc_start: 0.7745 (tptt) cc_final: 0.6396 (mttp) REVERT: A 529 LYS cc_start: 0.8247 (mppt) cc_final: 0.7889 (tmtm) REVERT: A 532 ASN cc_start: 0.8511 (t0) cc_final: 0.8257 (t0) REVERT: A 553 THR cc_start: 0.7517 (m) cc_final: 0.7148 (p) REVERT: A 646 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7998 (ttp-170) REVERT: A 755 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7489 (mt0) REVERT: A 825 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8246 (mttp) REVERT: A 957 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 994 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: B 205 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7201 (m) REVERT: B 226 LEU cc_start: 0.6154 (mt) cc_final: 0.5778 (mt) REVERT: B 237 ARG cc_start: 0.6699 (mtm-85) cc_final: 0.6265 (mtp85) REVERT: B 271 GLN cc_start: 0.7747 (mt0) cc_final: 0.7476 (mp10) REVERT: B 356 LYS cc_start: 0.8191 (tttp) cc_final: 0.7929 (tttt) REVERT: B 357 ARG cc_start: 0.8078 (ttt90) cc_final: 0.7665 (ttt90) REVERT: B 392 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: B 408 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7705 (ttp80) REVERT: B 424 LYS cc_start: 0.7490 (tptt) cc_final: 0.7243 (tppp) REVERT: B 508 TYR cc_start: 0.7749 (m-80) cc_final: 0.7490 (m-80) REVERT: B 556 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7154 (p0) REVERT: B 574 ASP cc_start: 0.7867 (t0) cc_final: 0.7551 (t0) REVERT: B 661 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8088 (mm-30) REVERT: B 663 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8569 (t0) REVERT: B 900 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8132 (mtp) REVERT: B 988 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7688 (mt-10) REVERT: B 1092 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: C 106 PHE cc_start: 0.5981 (m-80) cc_final: 0.5637 (m-80) REVERT: C 205 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7611 (m) REVERT: C 356 LYS cc_start: 0.8141 (tttp) cc_final: 0.7890 (tttt) REVERT: C 360 ASN cc_start: 0.8775 (m-40) cc_final: 0.7816 (t0) REVERT: C 424 LYS cc_start: 0.7320 (tptp) cc_final: 0.6566 (mttt) REVERT: C 463 PRO cc_start: 0.8720 (Cg_exo) cc_final: 0.8300 (Cg_endo) REVERT: C 556 ASN cc_start: 0.8015 (m-40) cc_final: 0.7388 (p0) REVERT: C 574 ASP cc_start: 0.7912 (t0) cc_final: 0.7420 (t0) REVERT: C 582 LEU cc_start: 0.8540 (mt) cc_final: 0.8278 (mm) REVERT: C 586 ASP cc_start: 0.7124 (m-30) cc_final: 0.6736 (m-30) REVERT: C 868 GLU cc_start: 0.8134 (mp0) cc_final: 0.7865 (tm-30) REVERT: C 964 LYS cc_start: 0.8753 (mttt) cc_final: 0.8245 (mmmt) REVERT: C 985 ASP cc_start: 0.7728 (p0) cc_final: 0.7518 (p0) outliers start: 56 outliers final: 24 residues processed: 240 average time/residue: 0.4875 time to fit residues: 139.2725 Evaluate side-chains 228 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 646 ARG Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR 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 531 THR 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 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU 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 760 CYS 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 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: 1.9990 chunk 158 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 901 GLN B 360 ASN B1106 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.188126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123167 restraints weight = 28259.832| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.26 r_work: 0.3357 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24285 Z= 0.153 Angle : 0.572 14.688 33147 Z= 0.288 Chirality : 0.044 0.238 3948 Planarity : 0.004 0.039 4155 Dihedral : 4.640 21.176 3099 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.35 % Allowed : 11.75 % Favored : 85.90 % 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: 0.25 (0.15), residues: 2844 helix: 1.47 (0.20), residues: 681 sheet: -0.01 (0.20), residues: 576 loop : -0.28 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.002 PHE B1121 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (24186) covalent geometry : angle 0.54945 / 0.28 (32886) SS BOND : bond 0.00619 / 0.41 ( 36) SS BOND : angle 2.06118 / 1.16 ( 72) hydrogen bonds : bond 0.03640 / 2.38 ( 1029) hydrogen bonds : angle 5.67815 / 3.92 ( 2814) link_BETA1-4 : bond 0.00273 / 0.15 ( 15) link_BETA1-4 : angle 1.08520 / 0.72 ( 45) link_NAG-ASN : bond 0.00256 / 0.16 ( 48) link_NAG-ASN : angle 1.99413 / 1.30 ( 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 268 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 0.874 Fit side-chains REVERT: A 356 LYS cc_start: 0.7983 (tttp) cc_final: 0.7639 (tttt) REVERT: A 357 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7834 (tpt-90) REVERT: A 367 VAL cc_start: 0.9044 (t) cc_final: 0.8843 (m) REVERT: A 424 LYS cc_start: 0.7715 (tptt) cc_final: 0.6467 (mttp) REVERT: A 529 LYS cc_start: 0.8277 (mppt) cc_final: 0.7907 (tmtm) REVERT: A 532 ASN cc_start: 0.8465 (t0) cc_final: 0.8224 (t0) REVERT: A 553 THR cc_start: 0.7583 (m) cc_final: 0.7204 (p) REVERT: A 558 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7703 (mmtm) REVERT: A 646 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7948 (ttp-170) REVERT: A 825 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8268 (mttp) REVERT: A 957 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: A 994 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: B 205 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7363 (m) REVERT: B 226 LEU cc_start: 0.6247 (mt) cc_final: 0.5780 (mt) REVERT: B 237 ARG cc_start: 0.6737 (mtm-85) cc_final: 0.6309 (mtp85) REVERT: B 271 GLN cc_start: 0.7641 (mt0) cc_final: 0.7436 (mp10) REVERT: B 356 LYS cc_start: 0.8204 (tttp) cc_final: 0.7923 (tttt) REVERT: B 357 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7660 (ttt90) REVERT: B 392 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: B 408 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7740 (ttp80) REVERT: B 424 LYS cc_start: 0.7521 (tptt) cc_final: 0.7250 (tppp) REVERT: B 508 TYR cc_start: 0.7767 (m-80) cc_final: 0.7485 (m-80) REVERT: B 556 ASN cc_start: 0.7530 (m-40) cc_final: 0.7238 (p0) REVERT: B 574 ASP cc_start: 0.7922 (t0) cc_final: 0.7597 (t0) REVERT: B 661 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8084 (mm-30) REVERT: B 663 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8595 (t0) REVERT: B 900 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8138 (mtp) REVERT: B 988 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 1092 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: C 106 PHE cc_start: 0.6143 (m-80) cc_final: 0.5874 (m-80) REVERT: C 118 LEU cc_start: 0.6585 (tt) cc_final: 0.6380 (tm) REVERT: C 356 LYS cc_start: 0.8160 (tttp) cc_final: 0.7886 (tttt) REVERT: C 359 SER cc_start: 0.8189 (p) cc_final: 0.7813 (t) REVERT: C 360 ASN cc_start: 0.8772 (m-40) cc_final: 0.8359 (m-40) REVERT: C 424 LYS cc_start: 0.7312 (tptp) cc_final: 0.6550 (mptt) REVERT: C 463 PRO cc_start: 0.8705 (Cg_exo) cc_final: 0.8245 (Cg_endo) REVERT: C 529 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (tttp) REVERT: C 556 ASN cc_start: 0.7982 (m-40) cc_final: 0.7389 (p0) REVERT: C 574 ASP cc_start: 0.7981 (t0) cc_final: 0.7459 (t0) REVERT: C 582 LEU cc_start: 0.8584 (mt) cc_final: 0.8333 (mm) REVERT: C 586 ASP cc_start: 0.7129 (m-30) cc_final: 0.6738 (m-30) REVERT: C 760 CYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5527 (t) REVERT: C 790 LYS cc_start: 0.8737 (pttt) cc_final: 0.8357 (pttp) REVERT: C 964 LYS cc_start: 0.8759 (mttt) cc_final: 0.8314 (mtpp) REVERT: C 994 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8189 (m-30) outliers start: 60 outliers final: 26 residues processed: 257 average time/residue: 0.4580 time to fit residues: 140.9614 Evaluate side-chains 226 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR 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 316 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 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 663 ASP 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 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 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: 5.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 901 GLN B 360 ASN C 314 GLN C 422 ASN C 901 GLN C1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.189331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123580 restraints weight = 28596.233| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.19 r_work: 0.3350 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24285 Z= 0.139 Angle : 0.555 14.371 33147 Z= 0.280 Chirality : 0.044 0.253 3948 Planarity : 0.004 0.042 4155 Dihedral : 4.525 20.359 3099 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.51 % Allowed : 12.22 % Favored : 85.27 % 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: 0.28 (0.15), residues: 2844 helix: 1.58 (0.20), residues: 681 sheet: 0.04 (0.20), residues: 594 loop : -0.33 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 408 TYR 0.025 0.001 TYR B 170 PHE 0.019 0.001 PHE A 318 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (24186) covalent geometry : angle 0.53500 / 0.27 (32886) SS BOND : bond 0.00482 / 0.29 ( 36) SS BOND : angle 1.90749 / 1.09 ( 72) hydrogen bonds : bond 0.03518 / 2.30 ( 1029) hydrogen bonds : angle 5.56792 / 3.85 ( 2814) link_BETA1-4 : bond 0.00279 / 0.15 ( 15) link_BETA1-4 : angle 1.00736 / 0.67 ( 45) link_NAG-ASN : bond 0.00256 / 0.17 ( 48) link_NAG-ASN : angle 1.86365 / 1.20 ( 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 264 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 1.012 Fit side-chains REVERT: A 357 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7675 (ptm160) REVERT: A 359 SER cc_start: 0.8214 (p) cc_final: 0.7555 (t) REVERT: A 360 ASN cc_start: 0.8444 (m-40) cc_final: 0.7882 (m110) REVERT: A 424 LYS cc_start: 0.7699 (tptt) cc_final: 0.6432 (mttp) REVERT: A 523 THR cc_start: 0.8720 (p) cc_final: 0.7787 (t) REVERT: A 529 LYS cc_start: 0.8316 (mppt) cc_final: 0.7909 (tmtm) REVERT: A 532 ASN cc_start: 0.8454 (t0) cc_final: 0.7965 (t0) REVERT: A 553 THR cc_start: 0.7507 (m) cc_final: 0.7139 (p) REVERT: A 558 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7793 (mmtm) REVERT: A 646 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7910 (ttp-170) REVERT: A 825 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8219 (mttp) REVERT: A 957 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 205 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7330 (m) REVERT: B 226 LEU cc_start: 0.6175 (mt) cc_final: 0.5712 (mt) REVERT: B 237 ARG cc_start: 0.6674 (mtm-85) cc_final: 0.6262 (mtp85) REVERT: B 271 GLN cc_start: 0.7611 (mt0) cc_final: 0.7409 (mp10) REVERT: B 356 LYS cc_start: 0.8201 (tttp) cc_final: 0.7922 (tttt) REVERT: B 357 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7673 (ttt90) REVERT: B 392 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: B 408 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7777 (ttp80) REVERT: B 424 LYS cc_start: 0.7488 (tptt) cc_final: 0.7229 (tppp) REVERT: B 508 TYR cc_start: 0.7764 (m-80) cc_final: 0.7560 (m-80) REVERT: B 529 LYS cc_start: 0.8214 (mppt) cc_final: 0.7780 (mmtt) REVERT: B 574 ASP cc_start: 0.7848 (t0) cc_final: 0.7494 (t0) REVERT: B 900 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8109 (mtp) REVERT: B 988 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 1092 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: B 1101 HIS cc_start: 0.7951 (m90) cc_final: 0.7681 (m90) REVERT: C 106 PHE cc_start: 0.6021 (m-80) cc_final: 0.5813 (m-80) REVERT: C 356 LYS cc_start: 0.8096 (tttp) cc_final: 0.7834 (tttt) REVERT: C 359 SER cc_start: 0.8150 (p) cc_final: 0.7778 (t) REVERT: C 360 ASN cc_start: 0.8771 (m-40) cc_final: 0.8362 (m-40) REVERT: C 422 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.5345 (p0) REVERT: C 424 LYS cc_start: 0.7307 (tptp) cc_final: 0.6546 (mttt) REVERT: C 463 PRO cc_start: 0.8746 (Cg_exo) cc_final: 0.8345 (Cg_endo) REVERT: C 529 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7553 (mppt) REVERT: C 556 ASN cc_start: 0.8014 (m-40) cc_final: 0.7344 (p0) REVERT: C 574 ASP cc_start: 0.7954 (t0) cc_final: 0.7414 (t0) REVERT: C 582 LEU cc_start: 0.8546 (mt) cc_final: 0.8299 (mm) REVERT: C 586 ASP cc_start: 0.7028 (m-30) cc_final: 0.6705 (m-30) REVERT: C 790 LYS cc_start: 0.8745 (pttt) cc_final: 0.8344 (pttp) REVERT: C 900 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: C 994 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8172 (m-30) outliers start: 64 outliers final: 32 residues processed: 246 average time/residue: 0.4539 time to fit residues: 134.2008 Evaluate side-chains 231 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 994 ASP 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 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR 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 B residue 1122 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 231 ILE 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 422 ASN 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 814 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 235 optimal weight: 0.0570 chunk 222 optimal weight: 9.9990 chunk 290 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 360 ASN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.186484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124854 restraints weight = 28714.064| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.22 r_work: 0.3397 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 24285 Z= 0.257 Angle : 0.650 14.707 33147 Z= 0.327 Chirality : 0.047 0.246 3948 Planarity : 0.004 0.038 4155 Dihedral : 4.786 20.574 3099 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.19 % Allowed : 12.81 % Favored : 85.00 % 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: 0.04 (0.15), residues: 2844 helix: 1.20 (0.20), residues: 678 sheet: -0.04 (0.19), residues: 606 loop : -0.42 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 408 TYR 0.022 0.002 TYR B 265 PHE 0.027 0.002 PHE B1121 TRP 0.011 0.002 TRP B1102 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (24186) covalent geometry : angle 0.62701 / 0.32 (32886) SS BOND : bond 0.00618 / 0.35 ( 36) SS BOND : angle 2.31051 / 1.38 ( 72) hydrogen bonds : bond 0.04072 / 2.65 ( 1029) hydrogen bonds : angle 5.90233 / 4.08 ( 2814) link_BETA1-4 : bond 0.00237 / 0.14 ( 15) link_BETA1-4 : angle 1.17751 / 0.78 ( 45) link_NAG-ASN : bond 0.00363 / 0.21 ( 48) link_NAG-ASN : angle 2.05562 / 1.32 ( 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 248 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8050 (tttp) cc_final: 0.7705 (tttt) REVERT: A 357 ARG cc_start: 0.8193 (ttt-90) cc_final: 0.7649 (tpt-90) REVERT: A 359 SER cc_start: 0.8213 (p) cc_final: 0.7765 (t) REVERT: A 424 LYS cc_start: 0.7707 (tptt) cc_final: 0.6471 (mttp) REVERT: A 529 LYS cc_start: 0.8314 (mppt) cc_final: 0.8009 (mppt) REVERT: A 553 THR cc_start: 0.7627 (m) cc_final: 0.7209 (p) REVERT: A 558 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7849 (mmtm) REVERT: A 646 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7996 (ttp-170) REVERT: A 825 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8251 (mttp) REVERT: A 957 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: A 994 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: B 190 ARG cc_start: 0.7332 (mtp180) cc_final: 0.6940 (ttp-170) REVERT: B 237 ARG cc_start: 0.6763 (mtm-85) cc_final: 0.6317 (mtp180) REVERT: B 319 ARG cc_start: 0.8318 (ptp-170) cc_final: 0.7938 (mtt180) REVERT: B 356 LYS cc_start: 0.8214 (tttp) cc_final: 0.7934 (tttt) REVERT: B 408 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7749 (ttp80) REVERT: B 424 LYS cc_start: 0.7546 (tptt) cc_final: 0.7301 (tppp) REVERT: B 508 TYR cc_start: 0.7744 (m-80) cc_final: 0.7487 (m-80) REVERT: B 556 ASN cc_start: 0.7533 (m-40) cc_final: 0.7209 (p0) REVERT: B 574 ASP cc_start: 0.7937 (t0) cc_final: 0.7625 (t0) REVERT: B 825 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8033 (mttt) REVERT: B 900 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: B 988 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7791 (mt-10) REVERT: B 1092 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: B 1101 HIS cc_start: 0.8029 (m90) cc_final: 0.7760 (m90) REVERT: C 106 PHE cc_start: 0.6266 (m-80) cc_final: 0.6034 (m-80) REVERT: C 239 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6461 (mm-40) REVERT: C 356 LYS cc_start: 0.8188 (tttp) cc_final: 0.7930 (tttt) REVERT: C 359 SER cc_start: 0.8159 (p) cc_final: 0.7831 (t) REVERT: C 360 ASN cc_start: 0.8660 (m-40) cc_final: 0.8255 (m-40) REVERT: C 422 ASN cc_start: 0.5653 (OUTLIER) cc_final: 0.5423 (p0) REVERT: C 529 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7702 (mppt) REVERT: C 556 ASN cc_start: 0.8032 (m-40) cc_final: 0.7372 (p0) REVERT: C 574 ASP cc_start: 0.8005 (t0) cc_final: 0.7449 (t0) REVERT: C 582 LEU cc_start: 0.8587 (mt) cc_final: 0.8375 (mm) REVERT: C 586 ASP cc_start: 0.7209 (m-30) cc_final: 0.6804 (m-30) REVERT: C 790 LYS cc_start: 0.8748 (pttt) cc_final: 0.8391 (pttp) REVERT: C 994 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: C 1092 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7835 (mt-10) outliers start: 56 outliers final: 30 residues processed: 233 average time/residue: 0.5252 time to fit residues: 145.3182 Evaluate side-chains 220 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 825 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 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 511 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR 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 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN 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 814 LYS 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 1092 GLU 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: 0.6980 chunk 112 optimal weight: 0.4980 chunk 206 optimal weight: 6.9990 chunk 63 optimal weight: 0.0870 chunk 223 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 901 GLN A 955 ASN B 188 ASN C 314 GLN C 422 ASN C 901 GLN C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.189319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128833 restraints weight = 28821.165| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.29 r_work: 0.3441 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24285 Z= 0.119 Angle : 0.545 14.656 33147 Z= 0.276 Chirality : 0.044 0.252 3948 Planarity : 0.004 0.039 4155 Dihedral : 4.469 19.290 3099 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.68 % Allowed : 13.87 % 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: 0.23 (0.15), residues: 2844 helix: 1.57 (0.20), residues: 684 sheet: -0.08 (0.20), residues: 576 loop : -0.34 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 408 TYR 0.026 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 A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (24186) covalent geometry : angle 0.52457 / 0.27 (32886) SS BOND : bond 0.00491 / 0.31 ( 36) SS BOND : angle 2.03018 / 1.21 ( 72) hydrogen bonds : bond 0.03413 / 2.23 ( 1029) hydrogen bonds : angle 5.54335 / 3.83 ( 2814) link_BETA1-4 : bond 0.00311 / 0.18 ( 15) link_BETA1-4 : angle 0.96923 / 0.65 ( 45) link_NAG-ASN : bond 0.00222 / 0.15 ( 48) link_NAG-ASN : angle 1.76092 / 1.13 ( 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 240 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 1.028 Fit side-chains REVERT: A 357 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7684 (ptm160) REVERT: A 359 SER cc_start: 0.8206 (p) cc_final: 0.7622 (t) REVERT: A 424 LYS cc_start: 0.7701 (tptt) cc_final: 0.6465 (mttp) REVERT: A 529 LYS cc_start: 0.8322 (mppt) cc_final: 0.8081 (mppt) REVERT: A 553 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7283 (p) REVERT: A 558 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7882 (mmtm) REVERT: A 578 ASP cc_start: 0.8111 (t0) cc_final: 0.7723 (t70) REVERT: A 646 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7953 (ttp-170) REVERT: A 825 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8243 (mttp) REVERT: A 957 GLN cc_start: 0.8685 (tp40) cc_final: 0.8458 (tt0) REVERT: B 226 LEU cc_start: 0.6202 (mt) cc_final: 0.5921 (mt) REVERT: B 237 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.6344 (mtp85) REVERT: B 319 ARG cc_start: 0.8290 (ptp-170) cc_final: 0.7942 (mtt180) REVERT: B 356 LYS cc_start: 0.8291 (tttp) cc_final: 0.8013 (tttt) REVERT: B 357 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7675 (ttt90) REVERT: B 408 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7359 (ppt90) REVERT: B 424 LYS cc_start: 0.7540 (tptt) cc_final: 0.7299 (tppp) REVERT: B 508 TYR cc_start: 0.7796 (m-80) cc_final: 0.7595 (m-80) REVERT: B 529 LYS cc_start: 0.8349 (mppt) cc_final: 0.8009 (mmtt) REVERT: B 574 ASP cc_start: 0.7931 (t0) cc_final: 0.7633 (t0) REVERT: B 661 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8100 (mm-30) REVERT: B 825 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8039 (mttt) REVERT: B 900 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: B 988 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 1092 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: C 118 LEU cc_start: 0.6618 (tt) cc_final: 0.6353 (tm) REVERT: C 239 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.5954 (mm-40) REVERT: C 356 LYS cc_start: 0.8248 (tttp) cc_final: 0.7988 (tttt) REVERT: C 359 SER cc_start: 0.8188 (p) cc_final: 0.7888 (t) REVERT: C 360 ASN cc_start: 0.8670 (m-40) cc_final: 0.8268 (m-40) REVERT: C 422 ASN cc_start: 0.5396 (OUTLIER) cc_final: 0.4698 (p0) REVERT: C 424 LYS cc_start: 0.7394 (tptp) cc_final: 0.6508 (mttt) REVERT: C 529 LYS cc_start: 0.8392 (tttp) cc_final: 0.7692 (mppt) REVERT: C 556 ASN cc_start: 0.8001 (m-40) cc_final: 0.7355 (p0) REVERT: C 574 ASP cc_start: 0.7925 (t0) cc_final: 0.7403 (t0) REVERT: C 582 LEU cc_start: 0.8615 (mt) cc_final: 0.8399 (mm) REVERT: C 586 ASP cc_start: 0.7168 (m-30) cc_final: 0.6843 (m-30) REVERT: C 790 LYS cc_start: 0.8750 (pttt) cc_final: 0.8374 (pttp) outliers start: 43 outliers final: 27 residues processed: 231 average time/residue: 0.5196 time to fit residues: 142.7830 Evaluate side-chains 223 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 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 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 511 VAL 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 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 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN 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 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 199 optimal weight: 10.0000 chunk 287 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 360 ASN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.187741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126197 restraints weight = 28712.933| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.25 r_work: 0.3407 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24285 Z= 0.196 Angle : 0.607 14.553 33147 Z= 0.305 Chirality : 0.046 0.427 3948 Planarity : 0.004 0.039 4155 Dihedral : 4.583 19.430 3099 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.84 % Allowed : 13.79 % Favored : 84.37 % 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: 0.18 (0.15), residues: 2844 helix: 1.43 (0.20), residues: 684 sheet: -0.01 (0.20), residues: 588 loop : -0.37 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 408 TYR 0.021 0.002 TYR B 170 PHE 0.023 0.002 PHE B 238 TRP 0.008 0.001 TRP B1102 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (24186) covalent geometry : angle 0.58284 / 0.30 (32886) SS BOND : bond 0.00596 / 0.34 ( 36) SS BOND : angle 2.46407 / 1.49 ( 72) hydrogen bonds : bond 0.03741 / 2.44 ( 1029) hydrogen bonds : angle 5.71950 / 3.97 ( 2814) link_BETA1-4 : bond 0.00259 / 0.15 ( 15) link_BETA1-4 : angle 1.05045 / 0.70 ( 45) link_NAG-ASN : bond 0.00301 / 0.19 ( 48) link_NAG-ASN : angle 1.94329 / 1.26 ( 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 235 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5831 (tt) REVERT: A 357 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7651 (tpt-90) REVERT: A 359 SER cc_start: 0.8212 (p) cc_final: 0.7734 (t) REVERT: A 424 LYS cc_start: 0.7673 (tptt) cc_final: 0.6437 (mttp) REVERT: A 529 LYS cc_start: 0.8308 (mppt) cc_final: 0.8006 (mppt) REVERT: A 553 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7205 (p) REVERT: A 558 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7868 (mmtm) REVERT: A 578 ASP cc_start: 0.8152 (t0) cc_final: 0.7739 (t70) REVERT: A 646 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7948 (ttp-170) REVERT: A 825 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8240 (mttp) REVERT: A 957 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: A 994 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: B 237 ARG cc_start: 0.6740 (mtm-85) cc_final: 0.6307 (mtp85) REVERT: B 319 ARG cc_start: 0.8299 (ptp-170) cc_final: 0.7928 (mtt180) REVERT: B 334 ASN cc_start: 0.7325 (m110) cc_final: 0.6879 (p0) REVERT: B 356 LYS cc_start: 0.8219 (tttp) cc_final: 0.7936 (tttt) REVERT: B 357 ARG cc_start: 0.8145 (ttt90) cc_final: 0.7651 (ttt90) REVERT: B 408 ARG cc_start: 0.7951 (ttp-110) cc_final: 0.7334 (ppt90) REVERT: B 424 LYS cc_start: 0.7499 (tptt) cc_final: 0.7238 (tppp) REVERT: B 508 TYR cc_start: 0.7717 (m-80) cc_final: 0.7507 (m-80) REVERT: B 574 ASP cc_start: 0.7926 (t0) cc_final: 0.7627 (t0) REVERT: B 661 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8114 (mm-30) REVERT: B 825 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8077 (mttt) REVERT: B 900 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: B 988 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 1092 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: C 118 LEU cc_start: 0.6578 (tt) cc_final: 0.6310 (tm) REVERT: C 239 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6502 (tp-100) REVERT: C 356 LYS cc_start: 0.8236 (tttp) cc_final: 0.7960 (tttt) REVERT: C 359 SER cc_start: 0.8164 (p) cc_final: 0.7838 (t) REVERT: C 360 ASN cc_start: 0.8644 (m-40) cc_final: 0.8240 (m-40) REVERT: C 396 TYR cc_start: 0.7912 (m-80) cc_final: 0.7639 (m-80) REVERT: C 408 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7570 (ppt170) REVERT: C 422 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5097 (p0) REVERT: C 556 ASN cc_start: 0.8037 (m-40) cc_final: 0.7402 (p0) REVERT: C 574 ASP cc_start: 0.7969 (t0) cc_final: 0.7400 (t0) REVERT: C 582 LEU cc_start: 0.8589 (mt) cc_final: 0.8371 (mm) REVERT: C 586 ASP cc_start: 0.7168 (m-30) cc_final: 0.6776 (m-30) REVERT: C 790 LYS cc_start: 0.8758 (pttt) cc_final: 0.8359 (pttp) REVERT: C 900 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8497 (mtm) outliers start: 47 outliers final: 26 residues processed: 222 average time/residue: 0.5333 time to fit residues: 140.9009 Evaluate side-chains 221 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU 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 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 62 VAL Chi-restraints excluded: chain B residue 166 CYS 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 511 VAL 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 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 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 218 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN C 314 GLN C 422 ASN C 532 ASN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.188746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127388 restraints weight = 28694.986| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.27 r_work: 0.3332 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24285 Z= 0.142 Angle : 0.563 14.499 33147 Z= 0.284 Chirality : 0.044 0.369 3948 Planarity : 0.004 0.038 4155 Dihedral : 4.461 19.525 3099 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.76 % Allowed : 13.87 % Favored : 84.37 % 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: 0.26 (0.15), residues: 2844 helix: 1.52 (0.20), residues: 687 sheet: -0.05 (0.20), residues: 570 loop : -0.28 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 408 TYR 0.023 0.001 TYR B 170 PHE 0.022 0.001 PHE B 238 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (24186) covalent geometry : angle 0.54041 / 0.28 (32886) SS BOND : bond 0.00507 / 0.31 ( 36) SS BOND : angle 2.23794 / 1.36 ( 72) hydrogen bonds : bond 0.03498 / 2.28 ( 1029) hydrogen bonds : angle 5.58379 / 3.87 ( 2814) link_BETA1-4 : bond 0.00287 / 0.17 ( 15) link_BETA1-4 : angle 0.97675 / 0.65 ( 45) link_NAG-ASN : bond 0.00280 / 0.19 ( 48) link_NAG-ASN : angle 1.84025 / 1.19 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8870.22 seconds wall clock time: 151 minutes 48.05 seconds (9108.05 seconds total)