Starting phenix.real_space_refine on Sun Sep 13 17:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xf5_22161/09_2026/6xf5_22161.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 105 5.16 5 C 15585 2.51 5 N 3984 2.21 5 O 4812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24486 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7882 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 50, 'TRANS': 958} Chain breaks: 7 Chain: "B" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7882 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 50, 'TRANS': 958} Chain breaks: 7 Chain: "C" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7882 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 50, 'TRANS': 958} Chain breaks: 7 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.64, per 1000 atoms: 0.23 Number of scatterers: 24486 At special positions: 0 Unit cell: (136.96, 132.68, 184.04, 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 105 16.00 O 4812 8.00 N 3984 7.00 C 15585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1315 " - " ASN A1074 " " NAG A1320 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1315 " - " ASN B1074 " " NAG B1320 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1315 " - " ASN C1074 " " NAG C1320 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 877.9 milliseconds 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 25.7% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.503A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.447A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.640A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.575A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.673A 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 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 945 through 965 removed outlier: 4.156A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.874A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1152 removed outlier: 3.509A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.503A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.446A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.575A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.765A 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 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 945 through 965 removed outlier: 4.155A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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: 4.341A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1152 removed outlier: 3.582A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B1152 " --> pdb=" O PHE B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.503A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.447A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.822A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.508A 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 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.330A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.156A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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: 4.229A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1152 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.584A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.655A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.737A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.612A 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: 4.160A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.162A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.932A 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: 3.511A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.513A 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 removed outlier: 3.516A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.452A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.052A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.170A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.585A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.737A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 4.031A 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 removed outlier: 6.612A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.160A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.162A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.931A 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 removed outlier: 3.512A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.516A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.452A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.052A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.800A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.800A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.170A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.585A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.736A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.612A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.160A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.162A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.517A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.452A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.052A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.685A 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 728 removed outlier: 6.801A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.170A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 993 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4253 1.33 - 1.45: 6808 1.45 - 1.57: 13830 1.57 - 1.69: 0 1.69 - 1.82: 129 Bond restraints: 25020 Sorted by residual: bond pdb=" N LYS B1149 " pdb=" CA LYS B1149 " ideal model delta sigma weight residual 1.459 1.504 -0.044 1.20e-02 6.94e+03 1.37e+01 bond pdb=" N GLN C1142 " pdb=" CA GLN C1142 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.32e+01 bond pdb=" N GLN A1142 " pdb=" CA GLN A1142 " ideal model delta sigma weight residual 1.462 1.494 -0.033 9.50e-03 1.11e+04 1.19e+01 bond pdb=" N VAL A1129 " pdb=" CA VAL A1129 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.22e-02 6.72e+03 1.12e+01 bond pdb=" N GLN B1142 " pdb=" CA GLN B1142 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.76e+00 ... (remaining 25015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 33155 2.46 - 4.91: 797 4.91 - 7.37: 72 7.37 - 9.83: 16 9.83 - 12.28: 1 Bond angle restraints: 34041 Sorted by residual: angle pdb=" C PRO A1143 " pdb=" CA PRO A1143 " pdb=" CB PRO A1143 " ideal model delta sigma weight residual 113.06 100.78 12.28 1.59e+00 3.96e-01 5.97e+01 angle pdb=" C LYS C 462 " pdb=" CA LYS C 462 " pdb=" CB LYS C 462 " ideal model delta sigma weight residual 108.86 118.00 -9.14 1.44e+00 4.82e-01 4.03e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.44 -7.74 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.86 -7.16 1.22e+00 6.72e-01 3.44e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.79 -6.09 1.22e+00 6.72e-01 2.49e+01 ... (remaining 34036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 13424 18.09 - 36.18: 768 36.18 - 54.26: 180 54.26 - 72.35: 34 72.35 - 90.44: 24 Dihedral angle restraints: 14430 sinusoidal: 5622 harmonic: 8808 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -176.44 90.44 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -176.41 90.41 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -176.38 90.38 1 1.00e+01 1.00e-02 9.66e+01 ... (remaining 14427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3258 0.066 - 0.133: 685 0.133 - 0.199: 80 0.199 - 0.266: 26 0.266 - 0.332: 4 Chirality restraints: 4053 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA GLU A1144 " pdb=" N GLU A1144 " pdb=" C GLU A1144 " pdb=" CB GLU A1144 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4050 not shown) Planarity restraints: 4377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.208 2.00e-02 2.50e+03 1.71e-01 3.64e+02 pdb=" C7 NAG B1304 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.277 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.165 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" C7 NAG B1307 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.122 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.219 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " -0.152 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG A1307 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " 0.201 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.021 2.00e-02 2.50e+03 ... (remaining 4374 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3551 2.77 - 3.30: 22118 3.30 - 3.83: 40614 3.83 - 4.37: 46708 4.37 - 4.90: 80858 Nonbonded interactions: 193849 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.234 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.235 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.236 3.040 ... (remaining 193844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 6.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.840 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.005 0.061 25119 Z= 0.323 Angle : 0.869 16.264 34299 Z= 0.527 Chirality : 0.056 0.332 4053 Planarity : 0.007 0.171 4329 Dihedral : 12.602 90.354 8637 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.53 % Allowed : 1.21 % Favored : 98.26 % Cbeta Deviations : 0.04 % 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: -0.31 (0.14), residues: 2979 helix: 1.19 (0.19), residues: 666 sheet: -0.04 (0.19), residues: 699 loop : -0.86 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 273 TYR 0.029 0.002 TYR B 505 PHE 0.042 0.002 PHE A 490 TRP 0.012 0.002 TRP C 104 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.32 (25020) covalent geometry : angle 0.85418 / 0.52 (34041) SS BOND : bond 0.00408 / 0.26 ( 39) SS BOND : angle 1.57933 / 1.01 ( 78) hydrogen bonds : bond 0.19070 / 12.31 ( 954) hydrogen bonds : angle 7.88698 / 5.43 ( 2763) link_BETA1-4 : bond 0.00651 / 0.40 ( 12) link_BETA1-4 : angle 1.29921 / 0.79 ( 36) link_NAG-ASN : bond 0.00610 / 0.47 ( 48) link_NAG-ASN : angle 2.39481 / 2.27 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8933 (mttt) cc_final: 0.8428 (mtmm) REVERT: A 564 GLN cc_start: 0.6954 (tp40) cc_final: 0.6231 (tp40) REVERT: B 378 LYS cc_start: 0.8952 (mttt) cc_final: 0.8414 (mtmm) REVERT: C 189 LEU cc_start: 0.8982 (tp) cc_final: 0.8771 (tp) outliers start: 14 outliers final: 2 residues processed: 199 average time/residue: 0.1770 time to fit residues: 55.3092 Evaluate side-chains 97 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 613 GLN B 66 HIS B 613 GLN C 66 HIS C 613 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.071809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050016 restraints weight = 107283.666| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.26 r_work: 0.2937 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25119 Z= 0.143 Angle : 0.565 12.010 34299 Z= 0.291 Chirality : 0.044 0.238 4053 Planarity : 0.005 0.062 4329 Dihedral : 4.336 29.746 3231 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.94 % Allowed : 5.81 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.15), residues: 2979 helix: 1.98 (0.20), residues: 675 sheet: 0.36 (0.18), residues: 705 loop : -0.64 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1019 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE B 92 TRP 0.005 0.001 TRP C 886 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (25020) covalent geometry : angle 0.54856 / 0.29 (34041) SS BOND : bond 0.00339 / 0.23 ( 39) SS BOND : angle 1.34548 / 0.79 ( 78) hydrogen bonds : bond 0.04094 / 2.64 ( 954) hydrogen bonds : angle 5.79810 / 4.03 ( 2763) link_BETA1-4 : bond 0.00282 / 0.17 ( 12) link_BETA1-4 : angle 0.86187 / 0.55 ( 36) link_NAG-ASN : bond 0.00421 / 0.28 ( 48) link_NAG-ASN : angle 1.93693 / 1.79 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.9137 (mttt) cc_final: 0.8705 (mtmm) REVERT: A 564 GLN cc_start: 0.7335 (tp40) cc_final: 0.6418 (tp40) REVERT: B 378 LYS cc_start: 0.9074 (mttt) cc_final: 0.8658 (mppt) REVERT: B 410 ILE cc_start: 0.9372 (mm) cc_final: 0.9165 (mm) REVERT: C 378 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8412 (mmtm) REVERT: C 740 MET cc_start: 0.9311 (mmm) cc_final: 0.9007 (mmm) REVERT: C 1017 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8914 (tm-30) outliers start: 25 outliers final: 10 residues processed: 123 average time/residue: 0.1529 time to fit residues: 31.8970 Evaluate side-chains 96 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 736 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 59 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 255 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 271 optimal weight: 0.4980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 52 GLN B 394 ASN B 519 HIS B 901 GLN B 955 ASN C 52 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN C1142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.069659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048011 restraints weight = 109152.662| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.10 r_work: 0.2892 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25119 Z= 0.194 Angle : 0.567 11.666 34299 Z= 0.290 Chirality : 0.043 0.201 4053 Planarity : 0.004 0.043 4329 Dihedral : 4.183 18.043 3229 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.98 % Allowed : 7.40 % Favored : 91.62 % 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: 0.47 (0.15), residues: 2979 helix: 2.31 (0.20), residues: 681 sheet: 0.38 (0.18), residues: 696 loop : -0.59 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1019 TYR 0.018 0.001 TYR C1067 PHE 0.016 0.001 PHE C 559 TRP 0.035 0.001 TRP B 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (25020) covalent geometry : angle 0.55237 / 0.29 (34041) SS BOND : bond 0.00299 / 0.21 ( 39) SS BOND : angle 0.94086 / 0.57 ( 78) hydrogen bonds : bond 0.04231 / 2.75 ( 954) hydrogen bonds : angle 5.35994 / 3.73 ( 2763) link_BETA1-4 : bond 0.00118 / 0.08 ( 12) link_BETA1-4 : angle 1.02951 / 0.61 ( 36) link_NAG-ASN : bond 0.00414 / 0.28 ( 48) link_NAG-ASN : angle 1.92205 / 1.76 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 979 ASP cc_start: 0.9191 (t0) cc_final: 0.8978 (t0) outliers start: 26 outliers final: 10 residues processed: 111 average time/residue: 0.1512 time to fit residues: 29.2188 Evaluate side-chains 82 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 110 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 151 optimal weight: 0.0670 chunk 189 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.069088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.048014 restraints weight = 108766.153| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.03 r_work: 0.2890 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25119 Z= 0.150 Angle : 0.520 11.385 34299 Z= 0.266 Chirality : 0.043 0.195 4053 Planarity : 0.004 0.042 4329 Dihedral : 4.039 19.526 3229 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.21 % Allowed : 7.89 % Favored : 90.90 % 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: 0.51 (0.15), residues: 2979 helix: 2.29 (0.20), residues: 705 sheet: 0.21 (0.18), residues: 708 loop : -0.49 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.001 PHE B1148 TRP 0.012 0.001 TRP B 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (25020) covalent geometry : angle 0.50359 / 0.26 (34041) SS BOND : bond 0.00337 / 0.25 ( 39) SS BOND : angle 1.52810 / 0.88 ( 78) hydrogen bonds : bond 0.03719 / 2.39 ( 954) hydrogen bonds : angle 5.13209 / 3.59 ( 2763) link_BETA1-4 : bond 0.00225 / 0.13 ( 12) link_BETA1-4 : angle 0.85906 / 0.51 ( 36) link_NAG-ASN : bond 0.00362 / 0.25 ( 48) link_NAG-ASN : angle 1.71522 / 1.59 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8978 (mttt) cc_final: 0.8714 (mppt) REVERT: C 378 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8417 (mppt) REVERT: C 912 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8534 (p) REVERT: C 979 ASP cc_start: 0.9240 (t0) cc_final: 0.9029 (t0) outliers start: 32 outliers final: 16 residues processed: 108 average time/residue: 0.1414 time to fit residues: 26.6932 Evaluate side-chains 86 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 220 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.0070 chunk 260 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 171 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.8652 > 50:) chunk 276 optimal weight: 0.5980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN B 519 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.068526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.047525 restraints weight = 108928.763| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.00 r_work: 0.2871 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25119 Z= 0.151 Angle : 0.509 10.141 34299 Z= 0.259 Chirality : 0.043 0.183 4053 Planarity : 0.004 0.041 4329 Dihedral : 3.939 19.091 3229 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.21 % Allowed : 8.53 % Favored : 90.26 % 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: 0.58 (0.15), residues: 2979 helix: 2.32 (0.20), residues: 705 sheet: 0.34 (0.19), residues: 663 loop : -0.46 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 765 TYR 0.018 0.001 TYR C1067 PHE 0.010 0.001 PHE C 377 TRP 0.012 0.001 TRP B 104 HIS 0.003 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (25020) covalent geometry : angle 0.49454 / 0.26 (34041) SS BOND : bond 0.00216 / 0.15 ( 39) SS BOND : angle 1.16020 / 0.67 ( 78) hydrogen bonds : bond 0.03709 / 2.38 ( 954) hydrogen bonds : angle 4.98289 / 3.48 ( 2763) link_BETA1-4 : bond 0.00174 / 0.10 ( 12) link_BETA1-4 : angle 0.91907 / 0.53 ( 36) link_NAG-ASN : bond 0.00331 / 0.23 ( 48) link_NAG-ASN : angle 1.73637 / 1.56 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.9137 (mttt) cc_final: 0.8891 (mmtt) REVERT: B 378 LYS cc_start: 0.9007 (mttt) cc_final: 0.8754 (mppt) REVERT: C 473 TYR cc_start: 0.8546 (t80) cc_final: 0.7932 (t80) outliers start: 32 outliers final: 23 residues processed: 102 average time/residue: 0.1395 time to fit residues: 25.1192 Evaluate side-chains 91 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 265 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 519 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.066135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044970 restraints weight = 108978.592| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.97 r_work: 0.2793 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25119 Z= 0.253 Angle : 0.602 8.812 34299 Z= 0.306 Chirality : 0.044 0.174 4053 Planarity : 0.004 0.041 4329 Dihedral : 4.257 21.662 3229 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.81 % Allowed : 8.61 % Favored : 89.58 % 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: 0.41 (0.15), residues: 2979 helix: 2.20 (0.20), residues: 702 sheet: 0.20 (0.18), residues: 663 loop : -0.55 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1019 TYR 0.017 0.001 TYR C1067 PHE 0.017 0.002 PHE B 559 TRP 0.005 0.001 TRP B 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 (25020) covalent geometry : angle 0.58752 / 0.30 (34041) SS BOND : bond 0.00333 / 0.22 ( 39) SS BOND : angle 1.54158 / 0.93 ( 78) hydrogen bonds : bond 0.04210 / 2.71 ( 954) hydrogen bonds : angle 5.18881 / 3.61 ( 2763) link_BETA1-4 : bond 0.00188 / 0.12 ( 12) link_BETA1-4 : angle 1.01250 / 0.59 ( 36) link_NAG-ASN : bond 0.00405 / 0.26 ( 48) link_NAG-ASN : angle 1.80147 / 1.53 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 75 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8555 (t80) cc_final: 0.7861 (t80) REVERT: A 1144 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8859 (mp0) REVERT: B 378 LYS cc_start: 0.9013 (mttt) cc_final: 0.8784 (mppt) REVERT: C 473 TYR cc_start: 0.8530 (t80) cc_final: 0.7920 (t80) REVERT: C 912 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8648 (p) outliers start: 48 outliers final: 31 residues processed: 115 average time/residue: 0.1322 time to fit residues: 27.2682 Evaluate side-chains 101 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 243 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN B 519 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.045798 restraints weight = 108609.290| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.99 r_work: 0.2812 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25119 Z= 0.147 Angle : 0.520 9.430 34299 Z= 0.264 Chirality : 0.043 0.165 4053 Planarity : 0.004 0.041 4329 Dihedral : 4.025 20.526 3229 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.66 % Allowed : 9.32 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2979 helix: 2.37 (0.20), residues: 702 sheet: 0.20 (0.19), residues: 663 loop : -0.48 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.033 0.001 TYR A 369 PHE 0.012 0.001 PHE C 377 TRP 0.011 0.001 TRP B 104 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (25020) covalent geometry : angle 0.50794 / 0.26 (34041) SS BOND : bond 0.00233 / 0.16 ( 39) SS BOND : angle 1.05975 / 0.63 ( 78) hydrogen bonds : bond 0.03729 / 2.40 ( 954) hydrogen bonds : angle 4.97030 / 3.46 ( 2763) link_BETA1-4 : bond 0.00194 / 0.11 ( 12) link_BETA1-4 : angle 0.91771 / 0.53 ( 36) link_NAG-ASN : bond 0.00302 / 0.21 ( 48) link_NAG-ASN : angle 1.64294 / 1.40 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8516 (t80) cc_final: 0.7833 (t80) REVERT: B 378 LYS cc_start: 0.9026 (mttt) cc_final: 0.8792 (mppt) REVERT: B 762 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: B 1004 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9538 (tt) REVERT: C 473 TYR cc_start: 0.8491 (t80) cc_final: 0.7896 (t80) REVERT: C 912 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8583 (p) outliers start: 44 outliers final: 32 residues processed: 110 average time/residue: 0.1309 time to fit residues: 26.2329 Evaluate side-chains 104 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 160 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 519 HIS B 804 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.066093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045063 restraints weight = 109289.445| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.01 r_work: 0.2797 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25119 Z= 0.175 Angle : 0.545 8.700 34299 Z= 0.275 Chirality : 0.043 0.164 4053 Planarity : 0.004 0.040 4329 Dihedral : 4.033 20.734 3229 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.70 % Allowed : 9.51 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2979 helix: 2.33 (0.20), residues: 702 sheet: 0.14 (0.19), residues: 687 loop : -0.51 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.030 0.001 TYR A 369 PHE 0.013 0.001 PHE A 194 TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (25020) covalent geometry : angle 0.53387 / 0.27 (34041) SS BOND : bond 0.00274 / 0.19 ( 39) SS BOND : angle 1.01892 / 0.62 ( 78) hydrogen bonds : bond 0.03797 / 2.44 ( 954) hydrogen bonds : angle 4.93697 / 3.43 ( 2763) link_BETA1-4 : bond 0.00111 / 0.06 ( 12) link_BETA1-4 : angle 0.93374 / 0.54 ( 36) link_NAG-ASN : bond 0.00319 / 0.21 ( 48) link_NAG-ASN : angle 1.63662 / 1.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 74 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8507 (t80) cc_final: 0.7828 (t80) REVERT: B 378 LYS cc_start: 0.9022 (mttt) cc_final: 0.8807 (mppt) REVERT: B 473 TYR cc_start: 0.8498 (t80) cc_final: 0.7924 (t80) REVERT: B 759 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8289 (t80) REVERT: B 762 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: B 1004 LEU cc_start: 0.9804 (OUTLIER) cc_final: 0.9563 (tt) REVERT: C 191 GLU cc_start: 0.8458 (mp0) cc_final: 0.8211 (mp0) REVERT: C 473 TYR cc_start: 0.8544 (t80) cc_final: 0.7954 (t80) REVERT: C 573 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 900 MET cc_start: 0.9013 (mtp) cc_final: 0.8646 (mtt) REVERT: C 912 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8604 (p) outliers start: 45 outliers final: 30 residues processed: 113 average time/residue: 0.1316 time to fit residues: 26.6441 Evaluate side-chains 103 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 186 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.065074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044167 restraints weight = 110044.419| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.00 r_work: 0.2768 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25119 Z= 0.214 Angle : 0.588 9.353 34299 Z= 0.295 Chirality : 0.044 0.165 4053 Planarity : 0.004 0.041 4329 Dihedral : 4.216 22.083 3229 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.70 % Allowed : 9.74 % Favored : 88.56 % 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: 0.33 (0.15), residues: 2979 helix: 2.26 (0.20), residues: 702 sheet: 0.03 (0.19), residues: 681 loop : -0.61 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.051 0.001 TYR A 369 PHE 0.018 0.001 PHE C 192 TRP 0.007 0.001 TRP B 104 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (25020) covalent geometry : angle 0.57701 / 0.29 (34041) SS BOND : bond 0.00280 / 0.18 ( 39) SS BOND : angle 1.04827 / 0.64 ( 78) hydrogen bonds : bond 0.03998 / 2.57 ( 954) hydrogen bonds : angle 5.05072 / 3.51 ( 2763) link_BETA1-4 : bond 0.00114 / 0.07 ( 12) link_BETA1-4 : angle 0.93954 / 0.54 ( 36) link_NAG-ASN : bond 0.00317 / 0.21 ( 48) link_NAG-ASN : angle 1.68806 / 1.31 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 66 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8536 (t80) cc_final: 0.7831 (t80) REVERT: A 1144 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8886 (mp0) REVERT: B 473 TYR cc_start: 0.8484 (t80) cc_final: 0.7902 (t80) REVERT: B 759 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8213 (t80) REVERT: B 762 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: C 473 TYR cc_start: 0.8547 (t80) cc_final: 0.7952 (t80) REVERT: C 573 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8854 (p) REVERT: C 912 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8628 (p) outliers start: 45 outliers final: 34 residues processed: 105 average time/residue: 0.1334 time to fit residues: 26.1368 Evaluate side-chains 99 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 88 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 237 optimal weight: 0.2980 chunk 136 optimal weight: 0.0270 chunk 117 optimal weight: 9.9990 chunk 57 optimal weight: 0.0870 chunk 34 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 189 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046025 restraints weight = 108242.139| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.97 r_work: 0.2833 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25119 Z= 0.092 Angle : 0.516 10.120 34299 Z= 0.256 Chirality : 0.043 0.172 4053 Planarity : 0.003 0.041 4329 Dihedral : 3.862 19.846 3229 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.06 % Allowed : 10.65 % Favored : 88.30 % 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: 0.52 (0.16), residues: 2979 helix: 2.56 (0.20), residues: 693 sheet: 0.22 (0.19), residues: 672 loop : -0.59 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.036 0.001 TYR A 369 PHE 0.022 0.001 PHE B 377 TRP 0.016 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (25020) covalent geometry : angle 0.50644 / 0.25 (34041) SS BOND : bond 0.00198 / 0.14 ( 39) SS BOND : angle 0.80425 / 0.49 ( 78) hydrogen bonds : bond 0.03419 / 2.18 ( 954) hydrogen bonds : angle 4.75715 / 3.31 ( 2763) link_BETA1-4 : bond 0.00289 / 0.17 ( 12) link_BETA1-4 : angle 0.90850 / 0.54 ( 36) link_NAG-ASN : bond 0.00301 / 0.21 ( 48) link_NAG-ASN : angle 1.47844 / 1.17 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 473 TYR cc_start: 0.8489 (t80) cc_final: 0.7834 (t80) REVERT: B 473 TYR cc_start: 0.8451 (t80) cc_final: 0.7888 (t80) REVERT: B 759 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8222 (t80) REVERT: B 762 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: C 473 TYR cc_start: 0.8469 (t80) cc_final: 0.7945 (t80) REVERT: C 900 MET cc_start: 0.8768 (mtp) cc_final: 0.8391 (mtt) REVERT: C 912 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8488 (p) outliers start: 28 outliers final: 21 residues processed: 93 average time/residue: 0.1350 time to fit residues: 22.9191 Evaluate side-chains 86 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 84 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.043945 restraints weight = 110147.970| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.99 r_work: 0.2763 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25119 Z= 0.242 Angle : 0.598 13.145 34299 Z= 0.300 Chirality : 0.044 0.165 4053 Planarity : 0.004 0.041 4329 Dihedral : 4.095 21.847 3229 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.21 % Allowed : 10.61 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.35 (0.16), residues: 2979 helix: 2.25 (0.20), residues: 705 sheet: 0.03 (0.19), residues: 708 loop : -0.60 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 765 TYR 0.038 0.001 TYR A 369 PHE 0.017 0.001 PHE C 92 TRP 0.004 0.001 TRP B 104 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (25020) covalent geometry : angle 0.58293 / 0.30 (34041) SS BOND : bond 0.00287 / 0.18 ( 39) SS BOND : angle 1.75303 / 1.02 ( 78) hydrogen bonds : bond 0.04028 / 2.60 ( 954) hydrogen bonds : angle 5.01908 / 3.48 ( 2763) link_BETA1-4 : bond 0.00166 / 0.09 ( 12) link_BETA1-4 : angle 1.01416 / 0.59 ( 36) link_NAG-ASN : bond 0.00317 / 0.21 ( 48) link_NAG-ASN : angle 1.67875 / 1.27 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5251.33 seconds wall clock time: 91 minutes 12.28 seconds (5472.28 seconds total)