Starting phenix.real_space_refine on Mon Aug 10 02:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s70_19761/08_2026/8s70_19761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s70_19761/08_2026/8s70_19761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2026/8s70_19761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2026/8s70_19761.map" model { file = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2026/8s70_19761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2026/8s70_19761.cif" } resolution = 4.2 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= 0.004 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 112 5.49 5 Mg 16 5.21 5 S 160 5.16 5 C 25456 2.51 5 N 7136 2.21 5 O 8240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41120 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, F, H, J, L, N, P, R, U, W, Y, D, 0, 2, 4, E, G, I, K, M, O, Q, S, V, X, Z, T, 1, 3, 5 Time building chain proxies: 4.22, per 1000 atoms: 0.10 Number of scatterers: 41120 At special positions: 0 Unit cell: (127.358, 119.915, 321.703, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 P 112 15.00 Mg 16 11.99 O 8240 8.00 N 7136 7.00 C 25456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=45, symmetry=0 Number of additional bonds: simple=45, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.3 seconds 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9280 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 45.7% alpha, 15.2% beta 0 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'D' and resid 1 through 21 Processing helix chain 'D' and resid 22 through 25 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU D 76 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 106 Processing helix chain 'D' and resid 120 through 135 Processing helix chain 'D' and resid 150 through 156 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP D 310 " --> pdb=" O LYS D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 21 Processing helix chain 'A' and resid 22 through 25 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 165 through 185 removed outlier: 3.551A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 21 Processing helix chain 'C' and resid 22 through 25 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP C 310 " --> pdb=" O LYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 21 Processing helix chain 'F' and resid 22 through 25 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 150 through 156 Processing helix chain 'F' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY F 179 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 218 removed outlier: 3.830A pdb=" N PHE F 216 " --> pdb=" O ASN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP F 310 " --> pdb=" O LYS F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR F 321 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 21 Processing helix chain 'H' and resid 22 through 25 Processing helix chain 'H' and resid 43 through 50 Processing helix chain 'H' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU H 76 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 106 Processing helix chain 'H' and resid 120 through 135 Processing helix chain 'H' and resid 150 through 156 Processing helix chain 'H' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY H 179 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN H 180 " --> pdb=" O LYS H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE H 216 " --> pdb=" O ASN H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP H 310 " --> pdb=" O LYS H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR H 321 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE H 322 " --> pdb=" O LEU H 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 21 Processing helix chain 'J' and resid 22 through 25 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 106 Processing helix chain 'J' and resid 120 through 135 Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU J 169 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE J 216 " --> pdb=" O ASN J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP J 310 " --> pdb=" O LYS J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR J 321 " --> pdb=" O VAL J 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE J 322 " --> pdb=" O LEU J 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 21 Processing helix chain 'L' and resid 22 through 25 Processing helix chain 'L' and resid 43 through 50 Processing helix chain 'L' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU L 76 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 106 Processing helix chain 'L' and resid 120 through 135 Processing helix chain 'L' and resid 150 through 156 Processing helix chain 'L' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU L 169 " --> pdb=" O LEU L 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY L 179 " --> pdb=" O ARG L 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN L 180 " --> pdb=" O LYS L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP L 310 " --> pdb=" O LYS L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR L 321 " --> pdb=" O VAL L 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE L 322 " --> pdb=" O LEU L 318 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 21 Processing helix chain 'N' and resid 22 through 25 Processing helix chain 'N' and resid 43 through 50 Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU N 76 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER N 77 " --> pdb=" O THR N 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL N 78 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 106 Processing helix chain 'N' and resid 120 through 135 Processing helix chain 'N' and resid 150 through 156 Processing helix chain 'N' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU N 169 " --> pdb=" O LEU N 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY N 179 " --> pdb=" O ARG N 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN N 180 " --> pdb=" O LYS N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE N 216 " --> pdb=" O ASN N 212 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU N 272 " --> pdb=" O TYR N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP N 310 " --> pdb=" O LYS N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR N 321 " --> pdb=" O VAL N 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE N 322 " --> pdb=" O LEU N 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 21 Processing helix chain 'P' and resid 22 through 25 Processing helix chain 'P' and resid 43 through 50 Processing helix chain 'P' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU P 76 " --> pdb=" O THR P 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER P 77 " --> pdb=" O THR P 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL P 78 " --> pdb=" O LEU P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 106 Processing helix chain 'P' and resid 120 through 135 Processing helix chain 'P' and resid 150 through 156 Processing helix chain 'P' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN P 180 " --> pdb=" O LYS P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE P 216 " --> pdb=" O ASN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU P 272 " --> pdb=" O TYR P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP P 310 " --> pdb=" O LYS P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE P 322 " --> pdb=" O LEU P 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 21 Processing helix chain 'R' and resid 22 through 25 Processing helix chain 'R' and resid 43 through 50 Processing helix chain 'R' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER R 77 " --> pdb=" O THR R 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 106 Processing helix chain 'R' and resid 120 through 135 Processing helix chain 'R' and resid 150 through 156 Processing helix chain 'R' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY R 179 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN R 180 " --> pdb=" O LYS R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE R 216 " --> pdb=" O ASN R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU R 272 " --> pdb=" O TYR R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP R 310 " --> pdb=" O LYS R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE R 322 " --> pdb=" O LEU R 318 " (cutoff:3.500A) Processing helix chain 'U' and resid 1 through 21 Processing helix chain 'U' and resid 22 through 25 Processing helix chain 'U' and resid 43 through 50 Processing helix chain 'U' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU U 76 " --> pdb=" O THR U 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER U 77 " --> pdb=" O THR U 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 106 Processing helix chain 'U' and resid 120 through 135 Processing helix chain 'U' and resid 150 through 156 Processing helix chain 'U' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU U 169 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN U 180 " --> pdb=" O LYS U 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE U 216 " --> pdb=" O ASN U 212 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU U 272 " --> pdb=" O TYR U 268 " (cutoff:3.500A) Processing helix chain 'U' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP U 310 " --> pdb=" O LYS U 306 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR U 321 " --> pdb=" O VAL U 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE U 322 " --> pdb=" O LEU U 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 1 through 21 Processing helix chain 'W' and resid 22 through 25 Processing helix chain 'W' and resid 43 through 50 Processing helix chain 'W' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU W 76 " --> pdb=" O THR W 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER W 77 " --> pdb=" O THR W 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL W 78 " --> pdb=" O LEU W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 106 Processing helix chain 'W' and resid 120 through 135 Processing helix chain 'W' and resid 150 through 156 Processing helix chain 'W' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU W 169 " --> pdb=" O LEU W 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY W 179 " --> pdb=" O ARG W 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN W 180 " --> pdb=" O LYS W 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE W 216 " --> pdb=" O ASN W 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU W 272 " --> pdb=" O TYR W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP W 310 " --> pdb=" O LYS W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR W 321 " --> pdb=" O VAL W 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE W 322 " --> pdb=" O LEU W 318 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 21 Processing helix chain 'Y' and resid 22 through 25 Processing helix chain 'Y' and resid 43 through 50 Processing helix chain 'Y' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU Y 76 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER Y 77 " --> pdb=" O THR Y 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL Y 78 " --> pdb=" O LEU Y 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 106 Processing helix chain 'Y' and resid 120 through 135 Processing helix chain 'Y' and resid 150 through 156 Processing helix chain 'Y' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU Y 169 " --> pdb=" O LEU Y 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY Y 179 " --> pdb=" O ARG Y 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN Y 180 " --> pdb=" O LYS Y 176 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE Y 216 " --> pdb=" O ASN Y 212 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU Y 272 " --> pdb=" O TYR Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP Y 310 " --> pdb=" O LYS Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR Y 321 " --> pdb=" O VAL Y 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE Y 322 " --> pdb=" O LEU Y 318 " (cutoff:3.500A) Processing helix chain '0' and resid 1 through 21 Processing helix chain '0' and resid 22 through 25 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU 0 76 " --> pdb=" O THR 0 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 0 77 " --> pdb=" O THR 0 73 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL 0 78 " --> pdb=" O LEU 0 74 " (cutoff:3.500A) Processing helix chain '0' and resid 99 through 106 Processing helix chain '0' and resid 120 through 135 Processing helix chain '0' and resid 150 through 156 Processing helix chain '0' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU 0 169 " --> pdb=" O LEU 0 165 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY 0 179 " --> pdb=" O ARG 0 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN 0 180 " --> pdb=" O LYS 0 176 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE 0 216 " --> pdb=" O ASN 0 212 " (cutoff:3.500A) Processing helix chain '0' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU 0 272 " --> pdb=" O TYR 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP 0 310 " --> pdb=" O LYS 0 306 " (cutoff:3.500A) Processing helix chain '0' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR 0 321 " --> pdb=" O VAL 0 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 0 322 " --> pdb=" O LEU 0 318 " (cutoff:3.500A) Processing helix chain '2' and resid 1 through 21 Processing helix chain '2' and resid 22 through 25 Processing helix chain '2' and resid 43 through 50 Processing helix chain '2' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU 2 76 " --> pdb=" O THR 2 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 2 77 " --> pdb=" O THR 2 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL 2 78 " --> pdb=" O LEU 2 74 " (cutoff:3.500A) Processing helix chain '2' and resid 99 through 106 Processing helix chain '2' and resid 120 through 135 Processing helix chain '2' and resid 150 through 156 Processing helix chain '2' and resid 165 through 185 removed outlier: 3.551A pdb=" N LEU 2 169 " --> pdb=" O LEU 2 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY 2 179 " --> pdb=" O ARG 2 175 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN 2 180 " --> pdb=" O LYS 2 176 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE 2 216 " --> pdb=" O ASN 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU 2 272 " --> pdb=" O TYR 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP 2 310 " --> pdb=" O LYS 2 306 " (cutoff:3.500A) Processing helix chain '2' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR 2 321 " --> pdb=" O VAL 2 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 2 322 " --> pdb=" O LEU 2 318 " (cutoff:3.500A) Processing helix chain '4' and resid 1 through 21 Processing helix chain '4' and resid 22 through 25 Processing helix chain '4' and resid 43 through 50 Processing helix chain '4' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU 4 76 " --> pdb=" O THR 4 72 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER 4 77 " --> pdb=" O THR 4 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL 4 78 " --> pdb=" O LEU 4 74 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 106 Processing helix chain '4' and resid 120 through 135 Processing helix chain '4' and resid 150 through 156 Processing helix chain '4' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU 4 169 " --> pdb=" O LEU 4 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY 4 179 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN 4 180 " --> pdb=" O LYS 4 176 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE 4 216 " --> pdb=" O ASN 4 212 " (cutoff:3.500A) Processing helix chain '4' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU 4 272 " --> pdb=" O TYR 4 268 " (cutoff:3.500A) Processing helix chain '4' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP 4 310 " --> pdb=" O LYS 4 306 " (cutoff:3.500A) Processing helix chain '4' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR 4 321 " --> pdb=" O VAL 4 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 4 322 " --> pdb=" O LEU 4 318 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=2, first strand: chain 'D' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL D 142 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 191 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 60 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU D 222 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 62 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE D 224 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 64 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG D 226 " --> pdb=" O TYR D 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG D 221 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 227 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU D 240 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA D 229 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY D 238 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS D 231 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 236 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'D' and resid 285 through 286 Processing sheet with id=4, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=5, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.745A pdb=" N VAL A 142 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 191 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 60 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU A 222 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU A 62 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 224 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR A 64 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG A 226 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 227 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU A 240 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA A 229 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY A 238 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS A 231 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 236 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=7, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=8, first strand: chain 'C' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL C 142 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 191 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 60 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU C 222 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU C 62 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE C 224 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR C 64 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG C 226 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 227 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU C 240 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA C 229 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY C 238 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS C 231 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 236 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=10, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=11, first strand: chain 'F' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL F 142 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 191 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE F 60 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU F 222 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU F 62 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE F 224 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR F 64 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG F 226 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG F 221 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR F 227 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU F 240 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA F 229 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY F 238 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS F 231 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 236 " --> pdb=" O LYS F 231 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 285 through 286 Processing sheet with id=13, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=14, first strand: chain 'H' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL H 142 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 191 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE H 60 " --> pdb=" O VAL H 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU H 222 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU H 62 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE H 224 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 64 " --> pdb=" O ILE H 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG H 226 " --> pdb=" O TYR H 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG H 221 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR H 227 " --> pdb=" O GLU H 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU H 240 " --> pdb=" O THR H 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA H 229 " --> pdb=" O GLY H 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY H 238 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS H 231 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 236 " --> pdb=" O LYS H 231 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 285 through 286 Processing sheet with id=16, first strand: chain 'J' and resid 38 through 39 Processing sheet with id=17, first strand: chain 'J' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL J 142 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE J 191 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE J 60 " --> pdb=" O VAL J 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU J 222 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU J 62 " --> pdb=" O LEU J 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE J 224 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR J 64 " --> pdb=" O ILE J 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG J 226 " --> pdb=" O TYR J 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG J 221 " --> pdb=" O VAL J 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR J 227 " --> pdb=" O GLU J 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU J 240 " --> pdb=" O THR J 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA J 229 " --> pdb=" O GLY J 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY J 238 " --> pdb=" O ALA J 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS J 231 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL J 236 " --> pdb=" O LYS J 231 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'J' and resid 285 through 286 Processing sheet with id=19, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=20, first strand: chain 'L' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL L 142 " --> pdb=" O ILE L 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE L 191 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE L 60 " --> pdb=" O VAL L 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU L 222 " --> pdb=" O ILE L 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU L 62 " --> pdb=" O LEU L 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE L 224 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR L 64 " --> pdb=" O ILE L 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG L 226 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG L 221 " --> pdb=" O VAL L 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR L 227 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU L 240 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA L 229 " --> pdb=" O GLY L 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY L 238 " --> pdb=" O ALA L 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS L 231 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL L 236 " --> pdb=" O LYS L 231 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'L' and resid 285 through 286 Processing sheet with id=22, first strand: chain 'N' and resid 38 through 39 Processing sheet with id=23, first strand: chain 'N' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL N 142 " --> pdb=" O ILE N 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE N 191 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE N 60 " --> pdb=" O VAL N 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU N 222 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU N 62 " --> pdb=" O LEU N 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE N 224 " --> pdb=" O GLU N 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR N 64 " --> pdb=" O ILE N 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG N 226 " --> pdb=" O TYR N 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG N 221 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR N 227 " --> pdb=" O GLU N 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU N 240 " --> pdb=" O THR N 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA N 229 " --> pdb=" O GLY N 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY N 238 " --> pdb=" O ALA N 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS N 231 " --> pdb=" O VAL N 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL N 236 " --> pdb=" O LYS N 231 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'N' and resid 285 through 286 Processing sheet with id=25, first strand: chain 'P' and resid 38 through 39 Processing sheet with id=26, first strand: chain 'P' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL P 142 " --> pdb=" O ILE P 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE P 191 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE P 60 " --> pdb=" O VAL P 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU P 222 " --> pdb=" O ILE P 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU P 62 " --> pdb=" O LEU P 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE P 224 " --> pdb=" O GLU P 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR P 64 " --> pdb=" O ILE P 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG P 226 " --> pdb=" O TYR P 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG P 221 " --> pdb=" O VAL P 246 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR P 227 " --> pdb=" O GLU P 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU P 240 " --> pdb=" O THR P 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA P 229 " --> pdb=" O GLY P 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY P 238 " --> pdb=" O ALA P 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS P 231 " --> pdb=" O VAL P 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL P 236 " --> pdb=" O LYS P 231 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'P' and resid 285 through 286 Processing sheet with id=28, first strand: chain 'R' and resid 38 through 39 Processing sheet with id=29, first strand: chain 'R' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL R 142 " --> pdb=" O ILE R 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE R 191 " --> pdb=" O VAL R 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE R 60 " --> pdb=" O VAL R 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU R 222 " --> pdb=" O ILE R 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU R 62 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE R 224 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR R 64 " --> pdb=" O ILE R 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG R 226 " --> pdb=" O TYR R 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG R 221 " --> pdb=" O VAL R 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR R 227 " --> pdb=" O GLU R 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU R 240 " --> pdb=" O THR R 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA R 229 " --> pdb=" O GLY R 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY R 238 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS R 231 " --> pdb=" O VAL R 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL R 236 " --> pdb=" O LYS R 231 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'R' and resid 285 through 286 Processing sheet with id=31, first strand: chain 'U' and resid 38 through 39 Processing sheet with id=32, first strand: chain 'U' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL U 142 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE U 191 " --> pdb=" O VAL U 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE U 60 " --> pdb=" O VAL U 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU U 222 " --> pdb=" O ILE U 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU U 62 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE U 224 " --> pdb=" O GLU U 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR U 64 " --> pdb=" O ILE U 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG U 226 " --> pdb=" O TYR U 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG U 221 " --> pdb=" O VAL U 246 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR U 227 " --> pdb=" O GLU U 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU U 240 " --> pdb=" O THR U 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA U 229 " --> pdb=" O GLY U 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY U 238 " --> pdb=" O ALA U 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS U 231 " --> pdb=" O VAL U 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL U 236 " --> pdb=" O LYS U 231 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'U' and resid 285 through 286 Processing sheet with id=34, first strand: chain 'W' and resid 38 through 39 Processing sheet with id=35, first strand: chain 'W' and resid 89 through 93 removed outlier: 3.745A pdb=" N VAL W 142 " --> pdb=" O ILE W 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE W 191 " --> pdb=" O VAL W 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE W 60 " --> pdb=" O VAL W 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU W 222 " --> pdb=" O ILE W 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU W 62 " --> pdb=" O LEU W 222 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE W 224 " --> pdb=" O GLU W 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR W 64 " --> pdb=" O ILE W 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG W 226 " --> pdb=" O TYR W 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG W 221 " --> pdb=" O VAL W 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR W 227 " --> pdb=" O GLU W 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU W 240 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA W 229 " --> pdb=" O GLY W 238 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY W 238 " --> pdb=" O ALA W 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS W 231 " --> pdb=" O VAL W 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL W 236 " --> pdb=" O LYS W 231 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'W' and resid 285 through 286 Processing sheet with id=37, first strand: chain 'Y' and resid 38 through 39 Processing sheet with id=38, first strand: chain 'Y' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL Y 142 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE Y 191 " --> pdb=" O VAL Y 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE Y 60 " --> pdb=" O VAL Y 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU Y 222 " --> pdb=" O ILE Y 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU Y 62 " --> pdb=" O LEU Y 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE Y 224 " --> pdb=" O GLU Y 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR Y 64 " --> pdb=" O ILE Y 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG Y 226 " --> pdb=" O TYR Y 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG Y 221 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR Y 227 " --> pdb=" O GLU Y 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU Y 240 " --> pdb=" O THR Y 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA Y 229 " --> pdb=" O GLY Y 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY Y 238 " --> pdb=" O ALA Y 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS Y 231 " --> pdb=" O VAL Y 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL Y 236 " --> pdb=" O LYS Y 231 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'Y' and resid 285 through 286 Processing sheet with id=40, first strand: chain '0' and resid 38 through 39 Processing sheet with id=41, first strand: chain '0' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL 0 142 " --> pdb=" O ILE 0 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE 0 191 " --> pdb=" O VAL 0 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE 0 60 " --> pdb=" O VAL 0 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU 0 222 " --> pdb=" O ILE 0 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU 0 62 " --> pdb=" O LEU 0 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE 0 224 " --> pdb=" O GLU 0 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR 0 64 " --> pdb=" O ILE 0 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG 0 226 " --> pdb=" O TYR 0 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG 0 221 " --> pdb=" O VAL 0 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR 0 227 " --> pdb=" O GLU 0 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU 0 240 " --> pdb=" O THR 0 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA 0 229 " --> pdb=" O GLY 0 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY 0 238 " --> pdb=" O ALA 0 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS 0 231 " --> pdb=" O VAL 0 236 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL 0 236 " --> pdb=" O LYS 0 231 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain '0' and resid 285 through 286 Processing sheet with id=43, first strand: chain '2' and resid 38 through 39 Processing sheet with id=44, first strand: chain '2' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE 2 191 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE 2 60 " --> pdb=" O VAL 2 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU 2 222 " --> pdb=" O ILE 2 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU 2 62 " --> pdb=" O LEU 2 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE 2 224 " --> pdb=" O GLU 2 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR 2 64 " --> pdb=" O ILE 2 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG 2 226 " --> pdb=" O TYR 2 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG 2 221 " --> pdb=" O VAL 2 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR 2 227 " --> pdb=" O GLU 2 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU 2 240 " --> pdb=" O THR 2 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA 2 229 " --> pdb=" O GLY 2 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY 2 238 " --> pdb=" O ALA 2 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS 2 231 " --> pdb=" O VAL 2 236 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL 2 236 " --> pdb=" O LYS 2 231 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain '2' and resid 285 through 286 Processing sheet with id=46, first strand: chain '4' and resid 38 through 39 Processing sheet with id=47, first strand: chain '4' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL 4 142 " --> pdb=" O ILE 4 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE 4 191 " --> pdb=" O VAL 4 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE 4 60 " --> pdb=" O VAL 4 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU 4 222 " --> pdb=" O ILE 4 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU 4 62 " --> pdb=" O LEU 4 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE 4 224 " --> pdb=" O GLU 4 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR 4 64 " --> pdb=" O ILE 4 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG 4 226 " --> pdb=" O TYR 4 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG 4 221 " --> pdb=" O VAL 4 246 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR 4 227 " --> pdb=" O GLU 4 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU 4 240 " --> pdb=" O THR 4 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA 4 229 " --> pdb=" O GLY 4 238 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY 4 238 " --> pdb=" O ALA 4 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS 4 231 " --> pdb=" O VAL 4 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL 4 236 " --> pdb=" O LYS 4 231 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain '4' and resid 285 through 286 1904 hydrogen bonds defined for protein. 5472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 10.62 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 13856 1.36 - 1.51: 10149 1.51 - 1.65: 17435 1.65 - 1.80: 128 1.80 - 1.95: 144 Bond restraints: 41712 Sorted by residual: bond pdb=" O3B AGS R 402 " pdb=" PB AGS R 402 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O3B AGS 2 402 " pdb=" PB AGS 2 402 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3B AGS J 402 " pdb=" PB AGS J 402 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3B AGS L 402 " pdb=" PB AGS L 402 " ideal model delta sigma weight residual 1.673 1.573 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O3B AGS 0 402 " pdb=" PB AGS 0 402 " ideal model delta sigma weight residual 1.673 1.573 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 41707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 55777 2.52 - 5.04: 606 5.04 - 7.57: 113 7.57 - 10.09: 80 10.09 - 12.61: 16 Bond angle restraints: 56592 Sorted by residual: angle pdb=" N ILE P 52 " pdb=" CA ILE P 52 " pdb=" C ILE P 52 " ideal model delta sigma weight residual 113.20 108.82 4.38 9.60e-01 1.09e+00 2.08e+01 angle pdb=" N ILE F 52 " pdb=" CA ILE F 52 " pdb=" C ILE F 52 " ideal model delta sigma weight residual 113.20 108.83 4.37 9.60e-01 1.09e+00 2.08e+01 angle pdb=" N ILE R 52 " pdb=" CA ILE R 52 " pdb=" C ILE R 52 " ideal model delta sigma weight residual 113.20 108.83 4.37 9.60e-01 1.09e+00 2.07e+01 angle pdb=" N ILE C 52 " pdb=" CA ILE C 52 " pdb=" C ILE C 52 " ideal model delta sigma weight residual 113.20 108.83 4.37 9.60e-01 1.09e+00 2.07e+01 angle pdb=" N ILE L 52 " pdb=" CA ILE L 52 " pdb=" C ILE L 52 " ideal model delta sigma weight residual 113.20 108.84 4.36 9.60e-01 1.09e+00 2.07e+01 ... (remaining 56587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.64: 24000 26.64 - 53.28: 960 53.28 - 79.91: 336 79.91 - 106.55: 64 106.55 - 133.19: 96 Dihedral angle restraints: 25456 sinusoidal: 10816 harmonic: 14640 Sorted by residual: dihedral pdb=" O1A AGS L 402 " pdb=" O3A AGS L 402 " pdb=" PA AGS L 402 " pdb=" PB AGS L 402 " ideal model delta sinusoidal sigma weight residual 82.37 -50.82 133.19 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual 82.37 -50.79 133.16 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual 82.37 -50.79 133.16 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 25453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4990 0.052 - 0.105: 1304 0.105 - 0.157: 202 0.157 - 0.209: 0 0.209 - 0.262: 16 Chirality restraints: 6512 Sorted by residual: chirality pdb=" C3' AGS L 402 " pdb=" C2' AGS L 402 " pdb=" C4' AGS L 402 " pdb=" O3' AGS L 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' AGS J 402 " pdb=" C2' AGS J 402 " pdb=" C4' AGS J 402 " pdb=" O3' AGS J 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C3' AGS Y 402 " pdb=" C2' AGS Y 402 " pdb=" C4' AGS Y 402 " pdb=" O3' AGS Y 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 6509 not shown) Planarity restraints: 7120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 204 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO F 205 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN W 204 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO W 205 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO W 205 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO W 205 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN P 204 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO P 205 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO P 205 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 205 " 0.024 5.00e-02 4.00e+02 ... (remaining 7117 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 360 1.29 - 2.19: 1698 2.19 - 3.10: 35851 3.10 - 4.00: 113033 4.00 - 4.90: 191546 Warning: very small nonbonded interaction distances. Nonbonded interactions: 342488 Sorted by model distance: nonbonded pdb=" OG1 THR U 72 " pdb="MG MG W 401 " model vdw 0.390 2.170 nonbonded pdb=" OG1 THR N 72 " pdb="MG MG P 401 " model vdw 0.391 2.170 nonbonded pdb=" OG1 THR R 72 " pdb="MG MG U 401 " model vdw 0.391 2.170 nonbonded pdb=" OG1 THR F 72 " pdb="MG MG H 401 " model vdw 0.391 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG 0 401 " model vdw 0.391 2.170 ... (remaining 342483 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'D' selection = chain '0' selection = chain '2' selection = chain '4' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'T' selection = chain '1' selection = chain '3' selection = chain '5' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 40.460 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5016 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 : 0.020 0.700 41757 Z= 1.974 Angle : 0.792 12.610 56592 Z= 0.446 Chirality : 0.046 0.262 6512 Planarity : 0.004 0.044 7120 Dihedral : 18.425 133.188 16176 Min Nonbonded Distance : 0.390 Molprobity Statistics. All-atom Clashscore : 45.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 5216 helix: 1.44 (0.11), residues: 2240 sheet: 1.42 (0.19), residues: 816 loop : -0.80 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.009 0.001 TYR W 268 PHE 0.010 0.002 PHE 0 259 TRP 0.004 0.001 TRP U 289 HIS 0.005 0.001 HIS 2 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.29 (41712) covalent geometry : angle 0.79228 / 0.45 (56592) hydrogen bonds : bond 0.19642 / 13.01 ( 1904) hydrogen bonds : angle 7.40824 / 5.63 ( 5472) Misc. bond : bond 0.59462 / 38.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 889 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7550 (ttt) cc_final: 0.7294 (ttt) REVERT: A 180 ASN cc_start: 0.9016 (m-40) cc_final: 0.8260 (t0) REVERT: A 206 GLU cc_start: 0.8440 (mp0) cc_final: 0.8050 (mp0) REVERT: A 237 VAL cc_start: 0.8477 (p) cc_final: 0.7904 (p) REVERT: A 303 ASN cc_start: 0.9511 (m-40) cc_final: 0.9284 (t0) REVERT: C 98 LEU cc_start: 0.8815 (tp) cc_final: 0.8515 (pp) REVERT: C 130 MET cc_start: 0.8207 (ttt) cc_final: 0.6603 (ttt) REVERT: C 151 LYS cc_start: 0.9018 (ptmm) cc_final: 0.8586 (tppt) REVERT: C 201 MET cc_start: 0.6104 (pmm) cc_final: 0.5903 (pmm) REVERT: C 276 LEU cc_start: 0.8918 (mp) cc_final: 0.8673 (tp) REVERT: F 254 PHE cc_start: 0.5726 (m-80) cc_final: 0.5317 (m-10) REVERT: H 26 MET cc_start: 0.0118 (ptt) cc_final: -0.0427 (ptt) REVERT: H 242 ARG cc_start: 0.7504 (ttt-90) cc_final: 0.7119 (mmm160) REVERT: J 74 LEU cc_start: 0.6794 (tp) cc_final: 0.6555 (mt) REVERT: J 236 VAL cc_start: 0.6928 (m) cc_final: 0.5721 (p) REVERT: L 64 TYR cc_start: 0.6291 (p90) cc_final: 0.6026 (p90) REVERT: L 254 PHE cc_start: 0.7691 (m-80) cc_final: 0.7207 (m-80) REVERT: N 26 MET cc_start: 0.0280 (ptt) cc_final: -0.0088 (pmm) REVERT: N 27 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7562 (mtt180) REVERT: N 130 MET cc_start: 0.7529 (ttt) cc_final: 0.7253 (ttt) REVERT: N 180 ASN cc_start: 0.9410 (m-40) cc_final: 0.8788 (t0) REVERT: N 206 GLU cc_start: 0.8922 (mp0) cc_final: 0.8518 (mp0) REVERT: N 244 LYS cc_start: 0.9400 (tttt) cc_final: 0.9186 (tppt) REVERT: N 290 TYR cc_start: 0.9255 (m-80) cc_final: 0.8668 (m-80) REVERT: P 26 MET cc_start: -0.1811 (ptt) cc_final: -0.2575 (pmm) REVERT: P 130 MET cc_start: 0.6934 (ttt) cc_final: 0.6718 (ttt) REVERT: P 222 LEU cc_start: 0.7075 (mp) cc_final: 0.6707 (mm) REVERT: P 276 LEU cc_start: 0.9323 (mp) cc_final: 0.9075 (tp) REVERT: P 303 ASN cc_start: 0.9106 (m-40) cc_final: 0.8705 (t0) REVERT: R 26 MET cc_start: -0.1354 (ptt) cc_final: -0.1559 (ptp) REVERT: U 26 MET cc_start: -0.0584 (ptt) cc_final: -0.1986 (pmm) REVERT: U 301 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6965 (mmtt) REVERT: W 92 VAL cc_start: 0.7745 (p) cc_final: 0.7353 (m) REVERT: Y 66 PRO cc_start: 0.6633 (Cg_exo) cc_final: 0.6352 (Cg_endo) REVERT: D 27 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7737 (mtm-85) REVERT: D 30 ASP cc_start: 0.8589 (t70) cc_final: 0.8015 (t0) REVERT: D 64 TYR cc_start: 0.8293 (p90) cc_final: 0.7664 (p90) REVERT: D 130 MET cc_start: 0.8576 (ttt) cc_final: 0.8269 (ttt) REVERT: D 151 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9044 (tppt) REVERT: D 180 ASN cc_start: 0.9403 (m-40) cc_final: 0.8977 (t0) REVERT: D 190 PHE cc_start: 0.8976 (m-80) cc_final: 0.8488 (m-10) REVERT: D 206 GLU cc_start: 0.8827 (mp0) cc_final: 0.8408 (mp0) REVERT: D 268 TYR cc_start: 0.8541 (t80) cc_final: 0.8194 (t80) REVERT: 0 26 MET cc_start: -0.0497 (ptt) cc_final: -0.0785 (pmm) REVERT: 0 81 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8711 (mm-30) REVERT: 0 178 THR cc_start: 0.7609 (t) cc_final: 0.6619 (p) REVERT: 0 222 LEU cc_start: 0.7816 (mp) cc_final: 0.7569 (mm) REVERT: 0 252 PRO cc_start: 0.8296 (Cg_exo) cc_final: 0.8074 (Cg_endo) REVERT: 2 145 VAL cc_start: 0.5694 (t) cc_final: 0.5393 (t) REVERT: 4 26 MET cc_start: 0.2504 (ptt) cc_final: 0.2125 (pmm) REVERT: 4 64 TYR cc_start: 0.6700 (p90) cc_final: 0.6345 (p90) REVERT: 4 201 MET cc_start: 0.2346 (pmm) cc_final: 0.1840 (ptm) outliers start: 0 outliers final: 0 residues processed: 889 average time/residue: 0.3148 time to fit residues: 425.9299 Evaluate side-chains 597 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 260 GLN A 325 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 325 GLN F 83 GLN F 117 GLN ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 260 GLN L 325 GLN N 85 GLN N 117 GLN N 260 GLN N 325 GLN P 180 ASN P 325 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN W 325 GLN ** Y 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 192 ASN ** Y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 260 GLN D 325 GLN 0 117 GLN 0 279 GLN 0 299 GLN 0 303 ASN 0 325 GLN 2 303 ASN 2 325 GLN 4 325 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.085339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.070783 restraints weight = 277773.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.072317 restraints weight = 212114.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.073530 restraints weight = 168083.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.074473 restraints weight = 137391.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.075258 restraints weight = 115452.848| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 41757 Z= 0.259 Angle : 0.997 14.752 56592 Z= 0.502 Chirality : 0.066 0.610 6512 Planarity : 0.009 0.181 7120 Dihedral : 22.581 172.760 6816 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.44 % Allowed : 7.03 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 5216 helix: 0.79 (0.11), residues: 2288 sheet: 1.12 (0.18), residues: 816 loop : -1.02 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 225 TYR 0.023 0.003 TYR 0 268 PHE 0.029 0.003 PHE J 216 TRP 0.007 0.001 TRP Y 289 HIS 0.011 0.002 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.26 (41712) covalent geometry : angle 0.99732 / 0.50 (56592) hydrogen bonds : bond 0.05803 / 3.85 ( 1904) hydrogen bonds : angle 5.85859 / 4.42 ( 5472) Misc. bond : bond 0.00781 / 0.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 697 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7932 (ttt) cc_final: 0.7666 (ttt) REVERT: A 162 HIS cc_start: 0.7357 (m-70) cc_final: 0.6992 (m-70) REVERT: A 183 ASN cc_start: 0.9155 (m-40) cc_final: 0.8943 (m-40) REVERT: A 190 PHE cc_start: 0.9003 (m-10) cc_final: 0.8649 (m-10) REVERT: A 206 GLU cc_start: 0.8178 (mp0) cc_final: 0.7969 (mp0) REVERT: A 237 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8158 (p) REVERT: A 241 THR cc_start: 0.8605 (m) cc_final: 0.8373 (m) REVERT: A 268 TYR cc_start: 0.8710 (t80) cc_final: 0.8265 (t80) REVERT: A 317 VAL cc_start: 0.9214 (m) cc_final: 0.8801 (p) REVERT: C 109 ASN cc_start: 0.7173 (t0) cc_final: 0.6899 (t0) REVERT: C 201 MET cc_start: 0.6940 (pmm) cc_final: 0.6710 (pmm) REVERT: C 243 VAL cc_start: 0.8066 (t) cc_final: 0.7679 (m) REVERT: C 276 LEU cc_start: 0.8661 (mp) cc_final: 0.8400 (tp) REVERT: F 98 LEU cc_start: 0.5694 (pt) cc_final: 0.5356 (pt) REVERT: F 153 GLU cc_start: 0.3881 (mp0) cc_final: 0.3079 (mp0) REVERT: F 162 HIS cc_start: 0.7330 (m-70) cc_final: 0.6743 (m170) REVERT: F 197 LYS cc_start: 0.6235 (mmtt) cc_final: 0.5787 (mmtt) REVERT: H 9 LEU cc_start: 0.9488 (tp) cc_final: 0.9175 (tt) REVERT: H 26 MET cc_start: 0.0665 (ptt) cc_final: 0.0363 (ptt) REVERT: H 268 TYR cc_start: 0.5900 (t80) cc_final: 0.5404 (t80) REVERT: J 74 LEU cc_start: 0.7390 (tp) cc_final: 0.7069 (mt) REVERT: J 79 ILE cc_start: 0.4602 (mt) cc_final: 0.4386 (mt) REVERT: J 122 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7909 (tp30) REVERT: J 244 LYS cc_start: 0.7999 (tttt) cc_final: 0.7061 (tmtt) REVERT: J 290 TYR cc_start: 0.7868 (t80) cc_final: 0.7595 (t80) REVERT: L 125 LEU cc_start: 0.8307 (mm) cc_final: 0.7748 (mt) REVERT: L 126 GLU cc_start: 0.8670 (pt0) cc_final: 0.8312 (tp30) REVERT: L 221 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7151 (ttm-80) REVERT: L 242 ARG cc_start: 0.8419 (ttt-90) cc_final: 0.7680 (ttp80) REVERT: L 244 LYS cc_start: 0.8219 (tttt) cc_final: 0.7752 (tptp) REVERT: L 254 PHE cc_start: 0.8509 (m-80) cc_final: 0.7919 (m-80) REVERT: L 256 GLN cc_start: 0.8169 (pp30) cc_final: 0.7342 (pp30) REVERT: L 290 TYR cc_start: 0.7817 (m-80) cc_final: 0.7415 (m-80) REVERT: N 26 MET cc_start: 0.0282 (ptt) cc_final: 0.0029 (pmm) REVERT: N 27 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7589 (mtt90) REVERT: N 112 ASP cc_start: 0.9148 (t0) cc_final: 0.8832 (t0) REVERT: N 130 MET cc_start: 0.7318 (ttt) cc_final: 0.7009 (ttt) REVERT: N 155 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8518 (mm-30) REVERT: N 158 MET cc_start: 0.7582 (mtp) cc_final: 0.6725 (mmm) REVERT: N 162 HIS cc_start: 0.7956 (m170) cc_final: 0.7755 (m170) REVERT: N 206 GLU cc_start: 0.8838 (mp0) cc_final: 0.8533 (mp0) REVERT: P 26 MET cc_start: -0.1975 (ptt) cc_final: -0.2383 (pmm) REVERT: P 111 ASP cc_start: 0.7792 (m-30) cc_final: 0.7444 (m-30) REVERT: P 141 ILE cc_start: 0.7740 (mm) cc_final: 0.7517 (mp) REVERT: P 153 GLU cc_start: 0.8602 (tt0) cc_final: 0.8376 (tp30) REVERT: P 222 LEU cc_start: 0.7556 (mp) cc_final: 0.6908 (mm) REVERT: P 276 LEU cc_start: 0.9231 (mp) cc_final: 0.8956 (tp) REVERT: P 303 ASN cc_start: 0.9355 (m-40) cc_final: 0.8953 (t0) REVERT: P 314 ILE cc_start: 0.7618 (mm) cc_final: 0.7345 (mm) REVERT: R 26 MET cc_start: -0.1102 (ptt) cc_final: -0.1875 (pmm) REVERT: R 130 MET cc_start: 0.7918 (mmp) cc_final: 0.7407 (mmp) REVERT: R 148 LEU cc_start: 0.8192 (mp) cc_final: 0.7969 (tt) REVERT: R 162 HIS cc_start: 0.7406 (m-70) cc_final: 0.7110 (m-70) REVERT: U 26 MET cc_start: 0.0275 (ptt) cc_final: -0.0790 (pmm) REVERT: U 64 TYR cc_start: 0.6288 (p90) cc_final: 0.5762 (p90) REVERT: U 169 LEU cc_start: 0.0552 (OUTLIER) cc_final: -0.0381 (mt) REVERT: U 170 MET cc_start: 0.3639 (mmt) cc_final: 0.3259 (mmp) REVERT: U 268 TYR cc_start: 0.6222 (t80) cc_final: 0.5837 (t80) REVERT: U 301 LYS cc_start: 0.7674 (mmtm) cc_final: 0.7413 (mmtt) REVERT: Y 15 GLN cc_start: 0.9371 (tp-100) cc_final: 0.9107 (tp-100) REVERT: Y 26 MET cc_start: 0.3384 (pmm) cc_final: 0.2510 (pmm) REVERT: Y 64 TYR cc_start: 0.6756 (p90) cc_final: 0.6554 (p90) REVERT: Y 153 GLU cc_start: 0.7363 (tt0) cc_final: 0.6671 (mm-30) REVERT: Y 162 HIS cc_start: 0.5230 (m-70) cc_final: 0.4853 (m-70) REVERT: Y 197 LYS cc_start: 0.8795 (mmpt) cc_final: 0.7896 (mmpt) REVERT: Y 242 ARG cc_start: 0.8765 (ttt-90) cc_final: 0.8114 (ttp80) REVERT: Y 244 LYS cc_start: 0.7797 (tttt) cc_final: 0.7440 (tptp) REVERT: Y 254 PHE cc_start: 0.8315 (m-80) cc_final: 0.7935 (m-80) REVERT: Y 256 GLN cc_start: 0.7917 (pp30) cc_final: 0.7198 (pp30) REVERT: D 26 MET cc_start: 0.1230 (pmm) cc_final: 0.0798 (pmm) REVERT: D 27 ARG cc_start: 0.8359 (mtt180) cc_final: 0.7817 (mtm-85) REVERT: D 30 ASP cc_start: 0.8770 (t70) cc_final: 0.8118 (t0) REVERT: D 64 TYR cc_start: 0.8706 (p90) cc_final: 0.8054 (p90) REVERT: D 126 GLU cc_start: 0.8409 (pt0) cc_final: 0.7802 (pp20) REVERT: D 151 LYS cc_start: 0.9475 (ptmm) cc_final: 0.9028 (tppt) REVERT: D 158 MET cc_start: 0.8223 (mtp) cc_final: 0.7462 (mtp) REVERT: D 180 ASN cc_start: 0.9492 (m-40) cc_final: 0.9088 (p0) REVERT: D 190 PHE cc_start: 0.9363 (m-80) cc_final: 0.9062 (m-10) REVERT: D 206 GLU cc_start: 0.8878 (mp0) cc_final: 0.8536 (mp0) REVERT: D 216 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: D 268 TYR cc_start: 0.8879 (t80) cc_final: 0.8297 (t80) REVERT: 0 81 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8968 (mm-30) REVERT: 0 98 LEU cc_start: 0.8635 (pp) cc_final: 0.8081 (pp) REVERT: 0 148 LEU cc_start: 0.9247 (tt) cc_final: 0.9012 (tt) REVERT: 0 151 LYS cc_start: 0.9028 (ptmm) cc_final: 0.8792 (mmtt) REVERT: 0 154 ILE cc_start: 0.8436 (mt) cc_final: 0.8131 (mt) REVERT: 0 158 MET cc_start: 0.7724 (pmm) cc_final: 0.7335 (pmm) REVERT: 0 222 LEU cc_start: 0.8749 (mp) cc_final: 0.8369 (mm) REVERT: 0 268 TYR cc_start: 0.8623 (t80) cc_final: 0.8049 (t80) REVERT: 2 111 ASP cc_start: 0.6370 (m-30) cc_final: 0.5923 (m-30) REVERT: 2 162 HIS cc_start: 0.6436 (m-70) cc_final: 0.5894 (m-70) REVERT: 2 192 ASN cc_start: 0.7582 (m110) cc_final: 0.7256 (m110) REVERT: 4 26 MET cc_start: 0.3781 (ptt) cc_final: 0.3086 (pmm) REVERT: 4 64 TYR cc_start: 0.7791 (p90) cc_final: 0.7355 (p90) REVERT: 4 201 MET cc_start: 0.2093 (pmm) cc_final: 0.1549 (ptm) outliers start: 18 outliers final: 5 residues processed: 708 average time/residue: 0.2814 time to fit residues: 308.9104 Evaluate side-chains 540 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 532 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 90 optimal weight: 9.9990 chunk 452 optimal weight: 20.0000 chunk 459 optimal weight: 30.0000 chunk 281 optimal weight: 8.9990 chunk 395 optimal weight: 0.8980 chunk 445 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 507 optimal weight: 10.0000 chunk 490 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 310 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 325 GLN C 325 GLN F 162 HIS ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN L 19 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN ** N 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN P 135 ASN P 325 GLN R 83 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS R 279 GLN R 325 GLN ** U 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN U 325 GLN W 96 HIS W 325 GLN Y 260 GLN Y 325 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 15 GLN 0 279 GLN 0 303 ASN 0 325 GLN 2 192 ASN 2 303 ASN 2 325 GLN 4 325 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.082497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.067783 restraints weight = 267900.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.069283 restraints weight = 204629.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.070452 restraints weight = 162881.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.071427 restraints weight = 134320.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.072198 restraints weight = 113199.500| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 41757 Z= 0.210 Angle : 0.838 10.882 56592 Z= 0.427 Chirality : 0.056 0.477 6512 Planarity : 0.006 0.127 7120 Dihedral : 21.079 168.657 6816 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.78 % Allowed : 7.90 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.11), residues: 5216 helix: 0.62 (0.11), residues: 2288 sheet: 0.96 (0.18), residues: 800 loop : -1.16 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 242 TYR 0.102 0.004 TYR P 102 PHE 0.027 0.002 PHE 2 190 TRP 0.016 0.001 TRP A 289 HIS 0.008 0.002 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (41712) covalent geometry : angle 0.83757 / 0.43 (56592) hydrogen bonds : bond 0.04418 / 2.93 ( 1904) hydrogen bonds : angle 5.43598 / 4.09 ( 5472) Misc. bond : bond 0.01069 / 0.73 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 671 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7903 (ttt) cc_final: 0.7538 (ttt) REVERT: A 133 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7647 (ptp-110) REVERT: A 162 HIS cc_start: 0.7232 (m-70) cc_final: 0.6804 (m170) REVERT: A 190 PHE cc_start: 0.8942 (m-10) cc_final: 0.8660 (m-10) REVERT: A 259 PHE cc_start: 0.8792 (p90) cc_final: 0.8592 (p90) REVERT: A 268 TYR cc_start: 0.8420 (t80) cc_final: 0.8105 (t80) REVERT: A 289 TRP cc_start: 0.8915 (m100) cc_final: 0.8686 (m100) REVERT: A 320 LYS cc_start: 0.9490 (ptpp) cc_final: 0.9267 (ptpp) REVERT: C 61 VAL cc_start: 0.6725 (t) cc_final: 0.6429 (m) REVERT: C 109 ASN cc_start: 0.7366 (t0) cc_final: 0.7107 (t0) REVERT: C 162 HIS cc_start: 0.7128 (m170) cc_final: 0.6524 (m170) REVERT: C 174 LEU cc_start: 0.8948 (mt) cc_final: 0.8657 (mt) REVERT: C 201 MET cc_start: 0.7428 (pmm) cc_final: 0.7137 (pmm) REVERT: C 276 LEU cc_start: 0.8768 (mp) cc_final: 0.8564 (tp) REVERT: F 98 LEU cc_start: 0.6248 (pt) cc_final: 0.5968 (pt) REVERT: F 148 LEU cc_start: 0.8295 (tt) cc_final: 0.7999 (mm) REVERT: F 153 GLU cc_start: 0.4357 (mp0) cc_final: 0.4074 (mp0) REVERT: F 162 HIS cc_start: 0.7589 (m90) cc_final: 0.7023 (m170) REVERT: F 168 ARG cc_start: 0.6283 (ptp-170) cc_final: 0.6076 (ptp-110) REVERT: H 189 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6356 (mp) REVERT: H 196 MET cc_start: 0.4401 (mmp) cc_final: 0.3982 (mmm) REVERT: H 205 PRO cc_start: 0.2325 (Cg_endo) cc_final: 0.1598 (Cg_exo) REVERT: H 244 LYS cc_start: 0.8466 (tmtt) cc_final: 0.7855 (tmtt) REVERT: H 268 TYR cc_start: 0.5670 (t80) cc_final: 0.5286 (t80) REVERT: J 5 LYS cc_start: 0.8373 (tptt) cc_final: 0.8132 (tptt) REVERT: J 74 LEU cc_start: 0.7549 (tp) cc_final: 0.7159 (mt) REVERT: J 236 VAL cc_start: 0.7234 (p) cc_final: 0.6980 (t) REVERT: L 31 HIS cc_start: 0.8133 (t-170) cc_final: 0.7822 (t-170) REVERT: L 66 PRO cc_start: 0.7713 (Cg_exo) cc_final: 0.6783 (Cg_endo) REVERT: L 125 LEU cc_start: 0.8522 (mm) cc_final: 0.8083 (mt) REVERT: L 129 ASP cc_start: 0.7746 (m-30) cc_final: 0.7022 (m-30) REVERT: L 133 ARG cc_start: 0.7151 (mpt180) cc_final: 0.6583 (ptp-110) REVERT: L 242 ARG cc_start: 0.8408 (ttt-90) cc_final: 0.7716 (ttp80) REVERT: L 244 LYS cc_start: 0.8373 (tttt) cc_final: 0.7904 (tptp) REVERT: L 254 PHE cc_start: 0.8527 (m-80) cc_final: 0.7961 (m-80) REVERT: L 256 GLN cc_start: 0.8350 (pp30) cc_final: 0.7841 (pp30) REVERT: L 290 TYR cc_start: 0.7700 (m-80) cc_final: 0.7298 (m-80) REVERT: N 18 ARG cc_start: 0.9154 (ptp-170) cc_final: 0.8835 (ptp-170) REVERT: N 112 ASP cc_start: 0.9101 (t0) cc_final: 0.8797 (t0) REVERT: N 130 MET cc_start: 0.7484 (ttt) cc_final: 0.7213 (ttt) REVERT: N 155 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8547 (mm-30) REVERT: N 206 GLU cc_start: 0.8734 (mp0) cc_final: 0.8293 (mp0) REVERT: N 256 GLN cc_start: 0.9085 (pp30) cc_final: 0.8839 (pp30) REVERT: N 320 LYS cc_start: 0.9495 (ptpp) cc_final: 0.9216 (pttm) REVERT: P 88 THR cc_start: 0.8643 (p) cc_final: 0.8184 (t) REVERT: P 130 MET cc_start: 0.7723 (ttt) cc_final: 0.7501 (ttt) REVERT: P 148 LEU cc_start: 0.9131 (tt) cc_final: 0.8864 (pp) REVERT: P 153 GLU cc_start: 0.8602 (tt0) cc_final: 0.8368 (tp30) REVERT: P 162 HIS cc_start: 0.7707 (m170) cc_final: 0.6434 (m170) REVERT: P 222 LEU cc_start: 0.7793 (mp) cc_final: 0.7076 (mm) REVERT: P 245 VAL cc_start: 0.7954 (t) cc_final: 0.7658 (t) REVERT: P 268 TYR cc_start: 0.8159 (t80) cc_final: 0.7947 (t80) REVERT: P 276 LEU cc_start: 0.9239 (mp) cc_final: 0.8985 (tp) REVERT: P 303 ASN cc_start: 0.9341 (m-40) cc_final: 0.9049 (t0) REVERT: P 311 ASN cc_start: 0.7996 (p0) cc_final: 0.7708 (p0) REVERT: R 141 ILE cc_start: 0.6714 (mp) cc_final: 0.6487 (mp) REVERT: R 242 ARG cc_start: 0.8443 (ptt90) cc_final: 0.7984 (mtm110) REVERT: U 13 LEU cc_start: 0.9174 (mt) cc_final: 0.8800 (pp) REVERT: U 26 MET cc_start: 0.0118 (ptt) cc_final: -0.0711 (pmm) REVERT: U 196 MET cc_start: 0.6823 (mmp) cc_final: 0.6486 (mmm) REVERT: U 268 TYR cc_start: 0.6008 (t80) cc_final: 0.5710 (t80) REVERT: Y 15 GLN cc_start: 0.9373 (tp-100) cc_final: 0.9168 (tp-100) REVERT: Y 26 MET cc_start: 0.3088 (pmm) cc_final: 0.1254 (ppp) REVERT: Y 64 TYR cc_start: 0.6832 (p90) cc_final: 0.6603 (p90) REVERT: Y 197 LYS cc_start: 0.9144 (mmpt) cc_final: 0.8943 (mmmt) REVERT: Y 242 ARG cc_start: 0.8876 (ttt-90) cc_final: 0.8123 (ttp80) REVERT: Y 244 LYS cc_start: 0.8135 (tttt) cc_final: 0.7701 (tptp) REVERT: Y 254 PHE cc_start: 0.8332 (m-80) cc_final: 0.7975 (m-80) REVERT: Y 256 GLN cc_start: 0.7999 (pp30) cc_final: 0.7215 (pp30) REVERT: D 27 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8107 (mtm-85) REVERT: D 30 ASP cc_start: 0.8606 (t70) cc_final: 0.7962 (t0) REVERT: D 85 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8965 (tm-30) REVERT: D 105 LYS cc_start: 0.9374 (ptpt) cc_final: 0.9141 (pttm) REVERT: D 151 LYS cc_start: 0.9459 (ptmm) cc_final: 0.9009 (tppt) REVERT: D 158 MET cc_start: 0.7325 (mtp) cc_final: 0.6725 (mtp) REVERT: D 162 HIS cc_start: 0.7096 (m170) cc_final: 0.6737 (m170) REVERT: D 180 ASN cc_start: 0.9415 (m-40) cc_final: 0.8981 (p0) REVERT: D 190 PHE cc_start: 0.9402 (m-80) cc_final: 0.9008 (m-10) REVERT: D 244 LYS cc_start: 0.9309 (tppt) cc_final: 0.9099 (tppt) REVERT: D 268 TYR cc_start: 0.8549 (t80) cc_final: 0.7774 (t80) REVERT: 0 81 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8939 (mm-30) REVERT: 0 158 MET cc_start: 0.7773 (pmm) cc_final: 0.7491 (pmm) REVERT: 0 189 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8051 (mp) REVERT: 0 222 LEU cc_start: 0.8839 (mp) cc_final: 0.8418 (mm) REVERT: 0 252 PRO cc_start: 0.9150 (Cg_exo) cc_final: 0.8912 (Cg_endo) REVERT: 0 268 TYR cc_start: 0.8574 (t80) cc_final: 0.8256 (t80) REVERT: 2 28 MET cc_start: 0.4415 (mmp) cc_final: 0.4209 (mmp) REVERT: 2 111 ASP cc_start: 0.6478 (m-30) cc_final: 0.6071 (m-30) REVERT: 2 148 LEU cc_start: 0.8828 (mp) cc_final: 0.8617 (mp) REVERT: 2 162 HIS cc_start: 0.6978 (m-70) cc_final: 0.6364 (m-70) REVERT: 2 170 MET cc_start: 0.6109 (ppp) cc_final: 0.5864 (ppp) REVERT: 4 26 MET cc_start: 0.4476 (ptt) cc_final: 0.4221 (ptp) REVERT: 4 64 TYR cc_start: 0.7673 (p90) cc_final: 0.7257 (p90) REVERT: 4 201 MET cc_start: 0.1964 (pmm) cc_final: 0.1400 (ptm) outliers start: 32 outliers final: 4 residues processed: 701 average time/residue: 0.2751 time to fit residues: 300.5962 Evaluate side-chains 521 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 515 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 311 optimal weight: 0.8980 chunk 447 optimal weight: 4.9990 chunk 355 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 453 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN F 279 GLN F 325 GLN H 123 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 135 ASN J 325 GLN L 85 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 GLN N 166 GLN N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN P 180 ASN P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS R 212 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN W 325 GLN Y 180 ASN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN ** 0 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 279 GLN 0 299 GLN 0 303 ASN 0 325 GLN 2 117 GLN 2 123 GLN 2 325 GLN 4 162 HIS ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 325 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.078563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.064725 restraints weight = 282808.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.066127 restraints weight = 215485.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.067223 restraints weight = 171261.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.068098 restraints weight = 140959.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.068792 restraints weight = 118986.044| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 41757 Z= 0.260 Angle : 0.907 13.417 56592 Z= 0.451 Chirality : 0.053 0.387 6512 Planarity : 0.006 0.101 7120 Dihedral : 20.558 171.796 6816 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.17 % Allowed : 8.34 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.11), residues: 5216 helix: 0.39 (0.11), residues: 2288 sheet: 0.45 (0.18), residues: 832 loop : -1.39 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG H 221 TYR 0.116 0.007 TYR N 102 PHE 0.028 0.003 PHE U 190 TRP 0.011 0.001 TRP 0 289 HIS 0.013 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.26 (41712) covalent geometry : angle 0.90720 / 0.45 (56592) hydrogen bonds : bond 0.04456 / 3.01 ( 1904) hydrogen bonds : angle 5.51349 / 4.13 ( 5472) Misc. bond : bond 0.01509 / 0.96 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 654 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8857 (p90) cc_final: 0.8619 (p90) REVERT: A 162 HIS cc_start: 0.7238 (m-70) cc_final: 0.6899 (m170) REVERT: A 217 TYR cc_start: 0.8807 (m-80) cc_final: 0.8555 (m-10) REVERT: A 268 TYR cc_start: 0.8557 (t80) cc_final: 0.8189 (t80) REVERT: A 289 TRP cc_start: 0.9117 (m100) cc_final: 0.8317 (m100) REVERT: A 320 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9302 (ptpp) REVERT: C 130 MET cc_start: 0.8493 (ttp) cc_final: 0.7837 (ttt) REVERT: C 151 LYS cc_start: 0.9020 (ptmm) cc_final: 0.8799 (tppt) REVERT: C 162 HIS cc_start: 0.7337 (m170) cc_final: 0.6672 (m170) REVERT: C 174 LEU cc_start: 0.9058 (mt) cc_final: 0.8842 (mt) REVERT: C 276 LEU cc_start: 0.8845 (mp) cc_final: 0.8642 (tp) REVERT: F 153 GLU cc_start: 0.4926 (mp0) cc_final: 0.4596 (mp0) REVERT: F 162 HIS cc_start: 0.7955 (m90) cc_final: 0.7434 (m170) REVERT: F 189 ILE cc_start: 0.5573 (tt) cc_final: 0.5023 (mp) REVERT: F 196 MET cc_start: 0.4747 (tpt) cc_final: 0.4534 (tpt) REVERT: H 197 LYS cc_start: 0.7777 (mptt) cc_final: 0.7576 (mmtm) REVERT: H 268 TYR cc_start: 0.6264 (t80) cc_final: 0.5934 (t80) REVERT: H 291 SER cc_start: 0.4414 (m) cc_final: 0.4202 (m) REVERT: J 26 MET cc_start: 0.2002 (pmm) cc_final: 0.1266 (pmm) REVERT: J 74 LEU cc_start: 0.7931 (tp) cc_final: 0.7476 (mt) REVERT: J 244 LYS cc_start: 0.7362 (tptp) cc_final: 0.6535 (tptp) REVERT: L 31 HIS cc_start: 0.8347 (t-170) cc_final: 0.8049 (t-170) REVERT: L 62 GLU cc_start: 0.7641 (pt0) cc_final: 0.6865 (pt0) REVERT: L 119 ASP cc_start: 0.8520 (p0) cc_final: 0.8299 (p0) REVERT: L 125 LEU cc_start: 0.8566 (mm) cc_final: 0.8084 (mt) REVERT: L 126 GLU cc_start: 0.8822 (pt0) cc_final: 0.8475 (tp30) REVERT: L 129 ASP cc_start: 0.8004 (m-30) cc_final: 0.7159 (m-30) REVERT: L 133 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7382 (ptp-110) REVERT: L 143 ASP cc_start: 0.8671 (t0) cc_final: 0.8316 (t0) REVERT: L 242 ARG cc_start: 0.8639 (ttt-90) cc_final: 0.7782 (ttp80) REVERT: L 244 LYS cc_start: 0.8691 (tttt) cc_final: 0.8311 (tptp) REVERT: L 254 PHE cc_start: 0.8742 (m-80) cc_final: 0.8120 (m-80) REVERT: L 256 GLN cc_start: 0.8563 (pp30) cc_final: 0.7859 (pp30) REVERT: L 290 TYR cc_start: 0.8085 (m-80) cc_final: 0.7609 (m-80) REVERT: N 28 MET cc_start: 0.6591 (tpp) cc_final: 0.6286 (tpp) REVERT: N 112 ASP cc_start: 0.9176 (t0) cc_final: 0.8870 (t0) REVERT: N 155 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8544 (mm-30) REVERT: N 162 HIS cc_start: 0.7950 (m170) cc_final: 0.7661 (m170) REVERT: N 206 GLU cc_start: 0.8797 (mp0) cc_final: 0.8305 (mp0) REVERT: N 256 GLN cc_start: 0.9124 (pp30) cc_final: 0.8714 (pp30) REVERT: N 320 LYS cc_start: 0.9479 (ptpp) cc_final: 0.9247 (ptpp) REVERT: P 109 ASN cc_start: 0.8191 (t0) cc_final: 0.7960 (t0) REVERT: P 111 ASP cc_start: 0.7941 (m-30) cc_final: 0.7584 (m-30) REVERT: P 130 MET cc_start: 0.7598 (ttt) cc_final: 0.6669 (ttt) REVERT: P 145 VAL cc_start: 0.8489 (t) cc_final: 0.7929 (t) REVERT: P 148 LEU cc_start: 0.9109 (tt) cc_final: 0.8800 (mp) REVERT: P 153 GLU cc_start: 0.8766 (tt0) cc_final: 0.8455 (tp30) REVERT: P 158 MET cc_start: 0.7466 (pmm) cc_final: 0.7109 (pmm) REVERT: P 162 HIS cc_start: 0.7921 (m170) cc_final: 0.7205 (m170) REVERT: P 201 MET cc_start: 0.7968 (pmm) cc_final: 0.7676 (pmm) REVERT: P 252 PRO cc_start: 0.8966 (Cg_exo) cc_final: 0.8676 (Cg_endo) REVERT: P 268 TYR cc_start: 0.8394 (t80) cc_final: 0.8115 (t80) REVERT: P 276 LEU cc_start: 0.9323 (mp) cc_final: 0.9114 (tp) REVERT: P 303 ASN cc_start: 0.9482 (m-40) cc_final: 0.9188 (t0) REVERT: R 26 MET cc_start: -0.0379 (ptt) cc_final: -0.1016 (pmm) REVERT: R 130 MET cc_start: 0.7967 (mmp) cc_final: 0.6988 (mmp) REVERT: R 162 HIS cc_start: 0.8099 (m90) cc_final: 0.7847 (m-70) REVERT: U 13 LEU cc_start: 0.9268 (mt) cc_final: 0.8937 (pp) REVERT: U 26 MET cc_start: 0.1585 (ptt) cc_final: 0.0375 (pmm) REVERT: U 170 MET cc_start: 0.5430 (mpp) cc_final: 0.3725 (ttt) REVERT: U 268 TYR cc_start: 0.6841 (t80) cc_final: 0.6484 (t80) REVERT: W 290 TYR cc_start: 0.7566 (t80) cc_final: 0.7342 (t80) REVERT: Y 26 MET cc_start: 0.3964 (pmm) cc_final: 0.3191 (pmm) REVERT: Y 64 TYR cc_start: 0.7248 (p90) cc_final: 0.6835 (p90) REVERT: Y 125 LEU cc_start: 0.9312 (mm) cc_final: 0.8948 (mt) REVERT: Y 129 ASP cc_start: 0.8262 (t70) cc_final: 0.7903 (m-30) REVERT: Y 242 ARG cc_start: 0.9021 (ttt-90) cc_final: 0.8432 (ttp80) REVERT: Y 244 LYS cc_start: 0.8420 (tttt) cc_final: 0.7997 (tptp) REVERT: Y 254 PHE cc_start: 0.8510 (m-80) cc_final: 0.8126 (m-80) REVERT: Y 256 GLN cc_start: 0.8409 (pp30) cc_final: 0.7657 (pp30) REVERT: D 105 LYS cc_start: 0.9473 (ptpt) cc_final: 0.9224 (pttm) REVERT: D 126 GLU cc_start: 0.8725 (pt0) cc_final: 0.8229 (pp20) REVERT: D 151 LYS cc_start: 0.9483 (ptmm) cc_final: 0.9048 (tppt) REVERT: D 158 MET cc_start: 0.7477 (mtp) cc_final: 0.6931 (ptm) REVERT: D 162 HIS cc_start: 0.7224 (m170) cc_final: 0.6880 (m170) REVERT: D 180 ASN cc_start: 0.9390 (m-40) cc_final: 0.8961 (p0) REVERT: D 190 PHE cc_start: 0.9507 (m-80) cc_final: 0.9095 (m-10) REVERT: D 244 LYS cc_start: 0.9337 (tppt) cc_final: 0.8746 (tppt) REVERT: D 268 TYR cc_start: 0.8501 (t80) cc_final: 0.7713 (t80) REVERT: D 306 LYS cc_start: 0.9616 (pptt) cc_final: 0.9406 (ptmm) REVERT: D 307 TYR cc_start: 0.9612 (t80) cc_final: 0.9405 (t80) REVERT: 0 81 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9016 (mm-30) REVERT: 0 151 LYS cc_start: 0.9213 (ptpp) cc_final: 0.9005 (pttm) REVERT: 0 158 MET cc_start: 0.7876 (pmm) cc_final: 0.7537 (pmm) REVERT: 0 201 MET cc_start: 0.7023 (pmm) cc_final: 0.6781 (pmm) REVERT: 0 222 LEU cc_start: 0.8987 (mp) cc_final: 0.8432 (mm) REVERT: 0 262 LEU cc_start: 0.8574 (tp) cc_final: 0.8203 (pp) REVERT: 0 268 TYR cc_start: 0.8542 (t80) cc_final: 0.8332 (t80) REVERT: 2 162 HIS cc_start: 0.7413 (m-70) cc_final: 0.6862 (m-70) REVERT: 4 64 TYR cc_start: 0.7811 (p90) cc_final: 0.7410 (p90) REVERT: 4 201 MET cc_start: 0.1771 (pmm) cc_final: 0.1425 (ptm) outliers start: 7 outliers final: 1 residues processed: 661 average time/residue: 0.2735 time to fit residues: 284.2641 Evaluate side-chains 528 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 527 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 472 optimal weight: 9.9990 chunk 411 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 389 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 433 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS A 183 ASN A 325 GLN C 83 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN F 279 GLN F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 172 GLN N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN Y 162 HIS Y 325 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 162 HIS ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.078687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.064245 restraints weight = 266956.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.065641 restraints weight = 203705.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.066723 restraints weight = 163204.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.067596 restraints weight = 135762.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.068297 restraints weight = 115942.776| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 41757 Z= 0.211 Angle : 0.822 14.770 56592 Z= 0.414 Chirality : 0.052 0.390 6512 Planarity : 0.006 0.068 7120 Dihedral : 20.337 173.572 6816 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % 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: -0.59 (0.11), residues: 5216 helix: 0.26 (0.11), residues: 2304 sheet: 0.43 (0.18), residues: 816 loop : -1.40 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG R 133 TYR 0.117 0.005 TYR P 102 PHE 0.026 0.002 PHE J 216 TRP 0.029 0.002 TRP Y 289 HIS 0.008 0.002 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (41712) covalent geometry : angle 0.82246 / 0.41 (56592) hydrogen bonds : bond 0.04246 / 2.84 ( 1904) hydrogen bonds : angle 5.44260 / 4.08 ( 5472) Misc. bond : bond 0.01191 / 0.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 616 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8761 (ptm-80) REVERT: A 64 TYR cc_start: 0.8706 (p90) cc_final: 0.8263 (p90) REVERT: A 130 MET cc_start: 0.8623 (ttt) cc_final: 0.8360 (ttt) REVERT: A 183 ASN cc_start: 0.9083 (m110) cc_final: 0.8839 (m-40) REVERT: A 268 TYR cc_start: 0.8392 (t80) cc_final: 0.8118 (t80) REVERT: A 289 TRP cc_start: 0.8902 (m100) cc_final: 0.8277 (m100) REVERT: A 320 LYS cc_start: 0.9545 (ptpp) cc_final: 0.9328 (ptpp) REVERT: C 109 ASN cc_start: 0.7909 (t0) cc_final: 0.7660 (t0) REVERT: C 130 MET cc_start: 0.8354 (ttp) cc_final: 0.7733 (ttt) REVERT: C 151 LYS cc_start: 0.9173 (ptmm) cc_final: 0.8894 (tppt) REVERT: C 174 LEU cc_start: 0.9085 (mt) cc_final: 0.8862 (mt) REVERT: F 109 ASN cc_start: 0.6963 (t0) cc_final: 0.6748 (t0) REVERT: F 148 LEU cc_start: 0.8352 (mm) cc_final: 0.8004 (mp) REVERT: F 162 HIS cc_start: 0.8081 (m90) cc_final: 0.7675 (m170) REVERT: F 189 ILE cc_start: 0.5264 (tt) cc_final: 0.5021 (tt) REVERT: F 254 PHE cc_start: 0.7510 (m-10) cc_final: 0.7253 (m-10) REVERT: H 196 MET cc_start: 0.5221 (mmp) cc_final: 0.4368 (mmm) REVERT: H 197 LYS cc_start: 0.7778 (mptt) cc_final: 0.7485 (mmtm) REVERT: H 242 ARG cc_start: 0.7602 (tpt90) cc_final: 0.7360 (tpt90) REVERT: J 74 LEU cc_start: 0.8168 (tp) cc_final: 0.7852 (mt) REVERT: J 244 LYS cc_start: 0.7626 (tptp) cc_final: 0.7219 (tppt) REVERT: L 26 MET cc_start: 0.4972 (pmm) cc_final: 0.1882 (ppp) REVERT: L 28 MET cc_start: 0.7909 (mmp) cc_final: 0.7686 (mmp) REVERT: L 119 ASP cc_start: 0.8568 (p0) cc_final: 0.8247 (p0) REVERT: L 143 ASP cc_start: 0.8683 (t0) cc_final: 0.8402 (t0) REVERT: L 158 MET cc_start: 0.7953 (mmp) cc_final: 0.6752 (mmp) REVERT: L 254 PHE cc_start: 0.8785 (m-80) cc_final: 0.8304 (m-80) REVERT: L 256 GLN cc_start: 0.8735 (pp30) cc_final: 0.8277 (pp30) REVERT: N 28 MET cc_start: 0.6639 (tpp) cc_final: 0.6329 (tpp) REVERT: N 162 HIS cc_start: 0.7797 (m170) cc_final: 0.7576 (m170) REVERT: N 256 GLN cc_start: 0.9111 (pp30) cc_final: 0.8694 (pp30) REVERT: N 307 TYR cc_start: 0.9572 (t80) cc_final: 0.9359 (t80) REVERT: N 320 LYS cc_start: 0.9476 (ptpp) cc_final: 0.9222 (ptpp) REVERT: P 28 MET cc_start: 0.5604 (mmp) cc_final: 0.5071 (mmp) REVERT: P 112 ASP cc_start: 0.8473 (m-30) cc_final: 0.8145 (t0) REVERT: P 153 GLU cc_start: 0.8747 (tt0) cc_final: 0.8442 (tp30) REVERT: P 158 MET cc_start: 0.8011 (pmm) cc_final: 0.7560 (pmm) REVERT: P 162 HIS cc_start: 0.7923 (m170) cc_final: 0.7234 (m170) REVERT: P 303 ASN cc_start: 0.9433 (m-40) cc_final: 0.9162 (t0) REVERT: R 26 MET cc_start: -0.0088 (ptt) cc_final: -0.0632 (pmm) REVERT: R 162 HIS cc_start: 0.8468 (m90) cc_final: 0.8250 (m-70) REVERT: U 13 LEU cc_start: 0.9327 (mt) cc_final: 0.9029 (pp) REVERT: U 26 MET cc_start: 0.2563 (ptt) cc_final: 0.0931 (pmm) REVERT: U 268 TYR cc_start: 0.6309 (t80) cc_final: 0.5945 (t80) REVERT: W 5 LYS cc_start: 0.8542 (tptt) cc_final: 0.7945 (pttm) REVERT: W 112 ASP cc_start: 0.7340 (m-30) cc_final: 0.6998 (t0) REVERT: W 290 TYR cc_start: 0.7580 (t80) cc_final: 0.7315 (t80) REVERT: Y 26 MET cc_start: 0.4287 (pmm) cc_final: 0.3364 (pmm) REVERT: Y 64 TYR cc_start: 0.7370 (p90) cc_final: 0.7083 (p90) REVERT: Y 125 LEU cc_start: 0.9371 (mm) cc_final: 0.9000 (mt) REVERT: Y 129 ASP cc_start: 0.8342 (t70) cc_final: 0.7978 (m-30) REVERT: D 105 LYS cc_start: 0.9518 (ptpt) cc_final: 0.9273 (pttm) REVERT: D 126 GLU cc_start: 0.8757 (pt0) cc_final: 0.8235 (pp20) REVERT: D 130 MET cc_start: 0.9169 (ppp) cc_final: 0.8860 (ppp) REVERT: D 151 LYS cc_start: 0.9476 (ptmm) cc_final: 0.9056 (tppt) REVERT: D 158 MET cc_start: 0.8086 (mtm) cc_final: 0.7858 (ptp) REVERT: D 162 HIS cc_start: 0.7022 (m170) cc_final: 0.6707 (m170) REVERT: D 180 ASN cc_start: 0.9371 (m-40) cc_final: 0.8879 (p0) REVERT: D 190 PHE cc_start: 0.9559 (m-80) cc_final: 0.9132 (m-10) REVERT: D 268 TYR cc_start: 0.8424 (t80) cc_final: 0.7848 (t80) REVERT: D 289 TRP cc_start: 0.8581 (m100) cc_final: 0.8119 (m100) REVERT: D 306 LYS cc_start: 0.9637 (pptt) cc_final: 0.9408 (ptmm) REVERT: 0 162 HIS cc_start: 0.7726 (m90) cc_final: 0.7226 (m170) REVERT: 0 222 LEU cc_start: 0.8935 (mp) cc_final: 0.8375 (mm) REVERT: 2 162 HIS cc_start: 0.7366 (m90) cc_final: 0.6988 (m-70) REVERT: 4 64 TYR cc_start: 0.7653 (p90) cc_final: 0.7287 (p90) REVERT: 4 201 MET cc_start: 0.2079 (pmm) cc_final: 0.1495 (ptm) outliers start: 7 outliers final: 7 residues processed: 623 average time/residue: 0.2765 time to fit residues: 269.7361 Evaluate side-chains 500 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 493 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 457 optimal weight: 40.0000 chunk 385 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 375 optimal weight: 0.0980 chunk 22 optimal weight: 7.9990 chunk 460 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 279 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN F 279 GLN F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN L 85 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 ASN ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN P 279 GLN P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN Y 83 GLN Y 162 HIS ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 180 ASN 2 325 GLN 4 15 GLN ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.076324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.062186 restraints weight = 275396.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.063485 restraints weight = 211742.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.064480 restraints weight = 171219.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.065309 restraints weight = 144166.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.065916 restraints weight = 124393.107| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.9328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 41757 Z= 0.237 Angle : 0.873 17.995 56592 Z= 0.439 Chirality : 0.052 0.397 6512 Planarity : 0.006 0.086 7120 Dihedral : 20.489 179.889 6816 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.89 % 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: -0.70 (0.11), residues: 5216 helix: 0.21 (0.11), residues: 2240 sheet: 0.15 (0.18), residues: 832 loop : -1.38 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG R 133 TYR 0.111 0.006 TYR F 102 PHE 0.046 0.003 PHE H 216 TRP 0.015 0.001 TRP Y 289 HIS 0.012 0.002 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (41712) covalent geometry : angle 0.87327 / 0.44 (56592) hydrogen bonds : bond 0.04347 / 2.91 ( 1904) hydrogen bonds : angle 5.60217 / 4.17 ( 5472) Misc. bond : bond 0.01264 / 0.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 639 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8851 (ptp-170) REVERT: A 64 TYR cc_start: 0.8945 (p90) cc_final: 0.8450 (p90) REVERT: A 130 MET cc_start: 0.8727 (ttt) cc_final: 0.8423 (ttt) REVERT: A 183 ASN cc_start: 0.9034 (m110) cc_final: 0.8825 (m-40) REVERT: A 268 TYR cc_start: 0.8582 (t80) cc_final: 0.8216 (t80) REVERT: A 289 TRP cc_start: 0.9007 (m100) cc_final: 0.8319 (m100) REVERT: A 320 LYS cc_start: 0.9595 (ptpp) cc_final: 0.9372 (ptpp) REVERT: C 109 ASN cc_start: 0.7864 (t0) cc_final: 0.7643 (t0) REVERT: F 109 ASN cc_start: 0.7207 (t0) cc_final: 0.6980 (t0) REVERT: F 148 LEU cc_start: 0.8529 (mm) cc_final: 0.8301 (mm) REVERT: F 162 HIS cc_start: 0.8183 (m90) cc_final: 0.7821 (m-70) REVERT: F 170 MET cc_start: 0.8714 (mpp) cc_final: 0.8429 (mmm) REVERT: F 254 PHE cc_start: 0.8062 (m-10) cc_final: 0.7699 (m-10) REVERT: H 197 LYS cc_start: 0.8117 (mptt) cc_final: 0.7851 (mmtm) REVERT: H 201 MET cc_start: 0.6959 (mpp) cc_final: 0.6686 (mpp) REVERT: J 15 GLN cc_start: 0.9374 (tt0) cc_final: 0.8763 (tm-30) REVERT: J 16 ILE cc_start: 0.8925 (tp) cc_final: 0.8060 (tp) REVERT: J 26 MET cc_start: 0.2123 (pmm) cc_final: 0.1328 (pmm) REVERT: J 158 MET cc_start: 0.8015 (mpp) cc_final: 0.7608 (mpp) REVERT: J 244 LYS cc_start: 0.7917 (tptp) cc_final: 0.7487 (tppt) REVERT: J 258 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7763 (tp30) REVERT: J 259 PHE cc_start: 0.7469 (p90) cc_final: 0.6578 (p90) REVERT: L 26 MET cc_start: 0.5616 (pmm) cc_final: 0.2629 (ppp) REVERT: L 119 ASP cc_start: 0.8778 (p0) cc_final: 0.8530 (p0) REVERT: L 126 GLU cc_start: 0.8845 (pt0) cc_final: 0.8378 (pp20) REVERT: L 143 ASP cc_start: 0.8563 (t0) cc_final: 0.8247 (t0) REVERT: L 242 ARG cc_start: 0.8860 (ttt-90) cc_final: 0.8172 (ttp80) REVERT: L 254 PHE cc_start: 0.9093 (m-80) cc_final: 0.8772 (m-80) REVERT: L 256 GLN cc_start: 0.8848 (pp30) cc_final: 0.8405 (pp30) REVERT: N 28 MET cc_start: 0.6866 (tpp) cc_final: 0.6642 (tpp) REVERT: N 151 LYS cc_start: 0.9437 (ptpp) cc_final: 0.8975 (ptpp) REVERT: N 162 HIS cc_start: 0.7702 (m170) cc_final: 0.7366 (m170) REVERT: N 256 GLN cc_start: 0.9002 (pp30) cc_final: 0.8585 (pp30) REVERT: N 320 LYS cc_start: 0.9513 (ptpp) cc_final: 0.9264 (ptpp) REVERT: P 112 ASP cc_start: 0.8630 (m-30) cc_final: 0.8367 (t0) REVERT: P 153 GLU cc_start: 0.8818 (tt0) cc_final: 0.8462 (tp30) REVERT: P 303 ASN cc_start: 0.9462 (m-40) cc_final: 0.9242 (t0) REVERT: R 109 ASN cc_start: 0.7726 (t0) cc_final: 0.7378 (t0) REVERT: R 130 MET cc_start: 0.8368 (mmp) cc_final: 0.7671 (mmt) REVERT: R 135 ASN cc_start: 0.8564 (m-40) cc_final: 0.8246 (m-40) REVERT: R 148 LEU cc_start: 0.8711 (mt) cc_final: 0.8456 (tt) REVERT: R 162 HIS cc_start: 0.8589 (m90) cc_final: 0.8262 (m170) REVERT: U 26 MET cc_start: 0.3739 (ptt) cc_final: 0.1907 (pmm) REVERT: U 162 HIS cc_start: 0.8654 (m-70) cc_final: 0.8356 (m-70) REVERT: U 196 MET cc_start: 0.6433 (mmm) cc_final: 0.6201 (mmm) REVERT: U 291 SER cc_start: 0.6674 (m) cc_final: 0.6438 (m) REVERT: W 28 MET cc_start: 0.8710 (mmm) cc_final: 0.8332 (mmm) REVERT: W 112 ASP cc_start: 0.7957 (m-30) cc_final: 0.7367 (t0) REVERT: W 197 LYS cc_start: 0.9036 (mptt) cc_final: 0.8693 (mmtm) REVERT: W 290 TYR cc_start: 0.7614 (t80) cc_final: 0.7328 (t80) REVERT: Y 26 MET cc_start: 0.4955 (pmm) cc_final: 0.4487 (pmm) REVERT: Y 129 ASP cc_start: 0.8550 (t70) cc_final: 0.8226 (m-30) REVERT: Y 178 THR cc_start: 0.8728 (t) cc_final: 0.8460 (p) REVERT: Y 225 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.7682 (mmm-85) REVERT: Y 242 ARG cc_start: 0.8983 (ttt-90) cc_final: 0.8533 (tmm-80) REVERT: D 67 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8763 (mm-30) REVERT: D 91 PHE cc_start: 0.8897 (t80) cc_final: 0.8662 (t80) REVERT: D 126 GLU cc_start: 0.8851 (pt0) cc_final: 0.8413 (pp20) REVERT: D 151 LYS cc_start: 0.9488 (ptmm) cc_final: 0.9081 (tppt) REVERT: D 158 MET cc_start: 0.8128 (mtm) cc_final: 0.7902 (ptp) REVERT: D 162 HIS cc_start: 0.7036 (m170) cc_final: 0.6769 (m170) REVERT: D 180 ASN cc_start: 0.9373 (m-40) cc_final: 0.8836 (p0) REVERT: D 190 PHE cc_start: 0.9581 (m-80) cc_final: 0.9266 (m-10) REVERT: D 268 TYR cc_start: 0.8463 (t80) cc_final: 0.7883 (t80) REVERT: D 289 TRP cc_start: 0.8740 (m100) cc_final: 0.8308 (m100) REVERT: D 306 LYS cc_start: 0.9670 (pptt) cc_final: 0.9456 (ptmm) REVERT: 0 151 LYS cc_start: 0.9184 (pttm) cc_final: 0.8934 (mmmm) REVERT: 0 158 MET cc_start: 0.7899 (pmm) cc_final: 0.7503 (pmm) REVERT: 0 162 HIS cc_start: 0.7675 (m90) cc_final: 0.7136 (m170) REVERT: 0 222 LEU cc_start: 0.9066 (mp) cc_final: 0.8440 (mm) REVERT: 0 254 PHE cc_start: 0.9639 (m-10) cc_final: 0.9236 (m-80) REVERT: 2 162 HIS cc_start: 0.7945 (m90) cc_final: 0.7526 (m-70) REVERT: 2 174 LEU cc_start: 0.8270 (mp) cc_final: 0.7895 (tt) REVERT: 2 260 GLN cc_start: 0.6139 (mt0) cc_final: 0.5852 (mp10) REVERT: 4 201 MET cc_start: 0.1862 (pmm) cc_final: 0.1455 (ptm) outliers start: 1 outliers final: 0 residues processed: 640 average time/residue: 0.2756 time to fit residues: 275.0997 Evaluate side-chains 497 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 197 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 385 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 chunk 419 optimal weight: 0.1980 chunk 506 optimal weight: 20.0000 chunk 328 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 505 optimal weight: 0.5980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN C 279 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 HIS ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 204 ASN L 325 GLN N 325 GLN P 85 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN P 279 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 279 GLN R 325 GLN U 162 HIS ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN W 31 HIS ** W 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN Y 85 GLN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.074855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.060551 restraints weight = 281232.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.061954 restraints weight = 213041.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.063034 restraints weight = 169620.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.063909 restraints weight = 140210.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.064603 restraints weight = 119345.059| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.9775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 41757 Z= 0.179 Angle : 0.775 9.900 56592 Z= 0.394 Chirality : 0.050 0.302 6512 Planarity : 0.006 0.128 7120 Dihedral : 20.383 178.878 6816 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 (0.11), residues: 5216 helix: 0.32 (0.11), residues: 2240 sheet: 0.38 (0.19), residues: 784 loop : -1.29 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 255 TYR 0.116 0.005 TYR 2 102 PHE 0.024 0.002 PHE H 216 TRP 0.011 0.001 TRP 0 289 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (41712) covalent geometry : angle 0.77506 / 0.39 (56592) hydrogen bonds : bond 0.03948 / 2.67 ( 1904) hydrogen bonds : angle 5.47068 / 4.10 ( 5472) Misc. bond : bond 0.01096 / 0.71 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8837 (ptp-170) REVERT: A 64 TYR cc_start: 0.8851 (p90) cc_final: 0.8417 (p90) REVERT: A 130 MET cc_start: 0.8693 (ttt) cc_final: 0.8390 (ttt) REVERT: A 183 ASN cc_start: 0.9009 (m110) cc_final: 0.8784 (m-40) REVERT: A 237 VAL cc_start: 0.8745 (p) cc_final: 0.8526 (p) REVERT: A 268 TYR cc_start: 0.8474 (t80) cc_final: 0.8213 (t80) REVERT: A 289 TRP cc_start: 0.8972 (m100) cc_final: 0.8388 (m100) REVERT: C 109 ASN cc_start: 0.7804 (t0) cc_final: 0.7573 (t0) REVERT: C 130 MET cc_start: 0.8980 (ptp) cc_final: 0.8374 (ptm) REVERT: C 143 ASP cc_start: 0.7259 (t0) cc_final: 0.7029 (t0) REVERT: C 206 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8109 (mm-30) REVERT: C 259 PHE cc_start: 0.8034 (p90) cc_final: 0.7814 (p90) REVERT: F 98 LEU cc_start: 0.8235 (pp) cc_final: 0.7028 (pp) REVERT: F 109 ASN cc_start: 0.7264 (t0) cc_final: 0.7051 (t0) REVERT: F 254 PHE cc_start: 0.7946 (m-10) cc_final: 0.7591 (m-10) REVERT: H 196 MET cc_start: 0.5547 (mmp) cc_final: 0.4725 (mmm) REVERT: H 197 LYS cc_start: 0.8042 (mptt) cc_final: 0.7737 (mmtm) REVERT: H 201 MET cc_start: 0.6878 (mpp) cc_final: 0.6653 (mpp) REVERT: H 205 PRO cc_start: 0.3873 (Cg_exo) cc_final: 0.2811 (Cg_endo) REVERT: H 242 ARG cc_start: 0.7657 (tpt90) cc_final: 0.7185 (tpt90) REVERT: J 15 GLN cc_start: 0.9191 (tt0) cc_final: 0.8833 (tm-30) REVERT: J 16 ILE cc_start: 0.8870 (tp) cc_final: 0.8131 (tp) REVERT: J 26 MET cc_start: 0.2417 (pmm) cc_final: 0.1997 (pmm) REVERT: J 64 TYR cc_start: 0.7293 (p90) cc_final: 0.7087 (p90) REVERT: J 158 MET cc_start: 0.8071 (mpp) cc_final: 0.7740 (mpp) REVERT: J 244 LYS cc_start: 0.7911 (tptp) cc_final: 0.7495 (tppt) REVERT: J 258 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7728 (tp30) REVERT: J 259 PHE cc_start: 0.7498 (p90) cc_final: 0.6676 (p90) REVERT: L 26 MET cc_start: 0.5340 (pmm) cc_final: 0.3016 (ppp) REVERT: L 119 ASP cc_start: 0.8734 (p0) cc_final: 0.8493 (p0) REVERT: L 126 GLU cc_start: 0.8773 (pt0) cc_final: 0.8296 (pp20) REVERT: L 143 ASP cc_start: 0.8467 (t0) cc_final: 0.8196 (t0) REVERT: L 158 MET cc_start: 0.8067 (mmp) cc_final: 0.7378 (mmp) REVERT: L 242 ARG cc_start: 0.8865 (ttt-90) cc_final: 0.8192 (ttp80) REVERT: L 254 PHE cc_start: 0.8998 (m-80) cc_final: 0.8708 (m-80) REVERT: L 256 GLN cc_start: 0.8825 (pp30) cc_final: 0.8338 (pp30) REVERT: N 28 MET cc_start: 0.6816 (tpp) cc_final: 0.6607 (tpp) REVERT: N 151 LYS cc_start: 0.9283 (ptpp) cc_final: 0.9068 (ptpp) REVERT: N 162 HIS cc_start: 0.7692 (m170) cc_final: 0.7366 (m170) REVERT: N 256 GLN cc_start: 0.9007 (pp30) cc_final: 0.8593 (pp30) REVERT: N 320 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9270 (ptpp) REVERT: P 111 ASP cc_start: 0.8181 (m-30) cc_final: 0.7910 (m-30) REVERT: P 112 ASP cc_start: 0.8659 (m-30) cc_final: 0.8354 (t0) REVERT: P 153 GLU cc_start: 0.8782 (tt0) cc_final: 0.8317 (tp30) REVERT: P 158 MET cc_start: 0.8175 (pmm) cc_final: 0.7807 (pmm) REVERT: P 162 HIS cc_start: 0.7915 (m170) cc_final: 0.7577 (m170) REVERT: P 303 ASN cc_start: 0.9520 (m-40) cc_final: 0.9269 (t0) REVERT: R 26 MET cc_start: 0.0776 (ptt) cc_final: 0.0038 (pmm) REVERT: R 109 ASN cc_start: 0.7776 (t0) cc_final: 0.7434 (t0) REVERT: R 133 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8190 (mtm110) REVERT: R 135 ASN cc_start: 0.8587 (m-40) cc_final: 0.8296 (m-40) REVERT: R 148 LEU cc_start: 0.8622 (mt) cc_final: 0.8385 (tt) REVERT: R 185 ASN cc_start: 0.8120 (p0) cc_final: 0.7850 (t0) REVERT: R 242 ARG cc_start: 0.8851 (pmt-80) cc_final: 0.8495 (tpt90) REVERT: U 26 MET cc_start: 0.3215 (ptt) cc_final: 0.2913 (ptt) REVERT: U 162 HIS cc_start: 0.8421 (m90) cc_final: 0.8137 (m-70) REVERT: U 196 MET cc_start: 0.6630 (mmm) cc_final: 0.5731 (mmm) REVERT: U 291 SER cc_start: 0.6380 (m) cc_final: 0.6146 (m) REVERT: W 112 ASP cc_start: 0.8108 (m-30) cc_final: 0.7444 (t0) REVERT: W 153 GLU cc_start: 0.5480 (mt-10) cc_final: 0.5054 (mm-30) REVERT: W 197 LYS cc_start: 0.9023 (mptt) cc_final: 0.8612 (mppt) REVERT: W 290 TYR cc_start: 0.7650 (t80) cc_final: 0.7308 (t80) REVERT: Y 26 MET cc_start: 0.4086 (pmm) cc_final: 0.2939 (pmm) REVERT: Y 129 ASP cc_start: 0.8580 (t70) cc_final: 0.8279 (t0) REVERT: Y 178 THR cc_start: 0.8635 (t) cc_final: 0.8409 (p) REVERT: Y 206 GLU cc_start: 0.9130 (mp0) cc_final: 0.8835 (pm20) REVERT: Y 242 ARG cc_start: 0.8945 (ttt-90) cc_final: 0.8542 (tmm-80) REVERT: Y 244 LYS cc_start: 0.8681 (tttt) cc_final: 0.8365 (tptp) REVERT: Y 268 TYR cc_start: 0.8066 (t80) cc_final: 0.7553 (t80) REVERT: D 126 GLU cc_start: 0.8861 (pt0) cc_final: 0.8391 (pp20) REVERT: D 151 LYS cc_start: 0.9475 (ptmm) cc_final: 0.9049 (tppt) REVERT: D 162 HIS cc_start: 0.7007 (m170) cc_final: 0.6745 (m170) REVERT: D 180 ASN cc_start: 0.9338 (m-40) cc_final: 0.8805 (p0) REVERT: D 190 PHE cc_start: 0.9567 (m-80) cc_final: 0.9251 (m-10) REVERT: D 268 TYR cc_start: 0.8463 (t80) cc_final: 0.7897 (t80) REVERT: D 289 TRP cc_start: 0.8803 (m100) cc_final: 0.8378 (m100) REVERT: D 306 LYS cc_start: 0.9666 (pptt) cc_final: 0.9452 (ptmm) REVERT: 0 91 PHE cc_start: 0.9070 (t80) cc_final: 0.8706 (t80) REVERT: 0 151 LYS cc_start: 0.9148 (pttm) cc_final: 0.8941 (mmmm) REVERT: 0 158 MET cc_start: 0.7826 (pmm) cc_final: 0.7383 (pmm) REVERT: 0 162 HIS cc_start: 0.7813 (m90) cc_final: 0.7306 (m170) REVERT: 0 268 TYR cc_start: 0.8738 (t80) cc_final: 0.8329 (t80) REVERT: 2 162 HIS cc_start: 0.7994 (m90) cc_final: 0.7598 (m-70) REVERT: 2 174 LEU cc_start: 0.8399 (mp) cc_final: 0.7979 (tt) REVERT: 4 201 MET cc_start: 0.1690 (pmm) cc_final: 0.1398 (ptm) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.2745 time to fit residues: 265.3372 Evaluate side-chains 492 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 331 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 345 optimal weight: 30.0000 chunk 356 optimal weight: 9.9990 chunk 295 optimal weight: 0.0870 chunk 495 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 HIS ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 325 GLN H 123 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN P 279 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 303 ASN U 325 GLN W 31 HIS ** W 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 166 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 279 GLN 0 303 ASN 0 325 GLN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 325 GLN 4 15 GLN ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.071016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.056780 restraints weight = 265869.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.058148 restraints weight = 199282.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.059225 restraints weight = 158247.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.060057 restraints weight = 130590.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.060753 restraints weight = 111443.489| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 1.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 41757 Z= 0.243 Angle : 0.872 12.354 56592 Z= 0.444 Chirality : 0.053 0.287 6512 Planarity : 0.007 0.164 7120 Dihedral : 20.570 179.596 6816 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.11), residues: 5216 helix: 0.11 (0.11), residues: 2240 sheet: 0.02 (0.18), residues: 816 loop : -1.45 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 255 TYR 0.101 0.006 TYR N 102 PHE 0.034 0.003 PHE H 216 TRP 0.013 0.001 TRP 0 289 HIS 0.022 0.002 HIS H 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 (41712) covalent geometry : angle 0.87232 / 0.44 (56592) hydrogen bonds : bond 0.04459 / 3.01 ( 1904) hydrogen bonds : angle 5.73452 / 4.28 ( 5472) Misc. bond : bond 0.01038 / 0.66 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 635 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8970 (p90) cc_final: 0.8631 (p90) REVERT: A 130 MET cc_start: 0.8883 (ttt) cc_final: 0.8513 (ttt) REVERT: A 183 ASN cc_start: 0.9030 (m110) cc_final: 0.8817 (m-40) REVERT: A 268 TYR cc_start: 0.8552 (t80) cc_final: 0.8228 (t80) REVERT: A 289 TRP cc_start: 0.9032 (m100) cc_final: 0.8367 (m100) REVERT: C 109 ASN cc_start: 0.8111 (t0) cc_final: 0.7907 (t0) REVERT: C 130 MET cc_start: 0.8904 (ptp) cc_final: 0.8214 (ptm) REVERT: C 143 ASP cc_start: 0.7524 (t0) cc_final: 0.7310 (t0) REVERT: C 158 MET cc_start: 0.8361 (pmm) cc_final: 0.7941 (pmm) REVERT: C 217 TYR cc_start: 0.9181 (m-10) cc_final: 0.8966 (m-10) REVERT: F 113 LEU cc_start: 0.5500 (tp) cc_final: 0.5234 (tp) REVERT: F 182 LYS cc_start: 0.8345 (tptm) cc_final: 0.8142 (tmmt) REVERT: F 196 MET cc_start: 0.6178 (tpt) cc_final: 0.5557 (tpt) REVERT: F 254 PHE cc_start: 0.8540 (m-10) cc_final: 0.8131 (m-10) REVERT: H 26 MET cc_start: 0.4188 (ptt) cc_final: 0.3428 (ptm) REVERT: H 197 LYS cc_start: 0.8091 (mptt) cc_final: 0.7794 (mmtm) REVERT: H 242 ARG cc_start: 0.7598 (tpt90) cc_final: 0.7068 (tpt90) REVERT: J 26 MET cc_start: 0.2801 (pmm) cc_final: 0.2405 (pmm) REVERT: J 64 TYR cc_start: 0.7320 (p90) cc_final: 0.7058 (p90) REVERT: J 158 MET cc_start: 0.8303 (mpp) cc_final: 0.8065 (mpp) REVERT: J 244 LYS cc_start: 0.8026 (tptp) cc_final: 0.7684 (tppt) REVERT: J 259 PHE cc_start: 0.7621 (p90) cc_final: 0.6973 (p90) REVERT: L 26 MET cc_start: 0.5210 (pmm) cc_final: 0.2820 (ptt) REVERT: L 119 ASP cc_start: 0.8847 (p0) cc_final: 0.8633 (p0) REVERT: L 126 GLU cc_start: 0.8770 (pt0) cc_final: 0.8341 (pp20) REVERT: L 242 ARG cc_start: 0.8873 (ttt-90) cc_final: 0.8329 (ttp80) REVERT: L 254 PHE cc_start: 0.9129 (m-80) cc_final: 0.8882 (m-80) REVERT: N 18 ARG cc_start: 0.9201 (ptt-90) cc_final: 0.8949 (ptt180) REVERT: N 151 LYS cc_start: 0.9369 (ptpp) cc_final: 0.8935 (pttm) REVERT: N 162 HIS cc_start: 0.7595 (m170) cc_final: 0.7280 (m170) REVERT: N 256 GLN cc_start: 0.8932 (pp30) cc_final: 0.8561 (pp30) REVERT: N 268 TYR cc_start: 0.8351 (t80) cc_final: 0.8070 (t80) REVERT: N 290 TYR cc_start: 0.9303 (m-10) cc_final: 0.9091 (m-10) REVERT: P 153 GLU cc_start: 0.8779 (tt0) cc_final: 0.8559 (tm-30) REVERT: P 158 MET cc_start: 0.8327 (pmm) cc_final: 0.8019 (pmm) REVERT: P 222 LEU cc_start: 0.9353 (mt) cc_final: 0.9095 (mm) REVERT: P 268 TYR cc_start: 0.7956 (t80) cc_final: 0.7721 (t80) REVERT: R 7 ARG cc_start: 0.9434 (ppt170) cc_final: 0.9195 (ppt170) REVERT: R 109 ASN cc_start: 0.7971 (t0) cc_final: 0.7616 (t0) REVERT: R 133 ARG cc_start: 0.8741 (ptp90) cc_final: 0.8507 (mtm-85) REVERT: R 135 ASN cc_start: 0.8824 (m-40) cc_final: 0.8610 (m-40) REVERT: R 162 HIS cc_start: 0.8494 (m-70) cc_final: 0.8291 (m170) REVERT: R 242 ARG cc_start: 0.8852 (pmt-80) cc_final: 0.8149 (ttp80) REVERT: U 13 LEU cc_start: 0.9141 (pp) cc_final: 0.8708 (pp) REVERT: U 162 HIS cc_start: 0.8546 (m90) cc_final: 0.8197 (m-70) REVERT: U 196 MET cc_start: 0.7036 (mmm) cc_final: 0.6053 (mmm) REVERT: W 7 ARG cc_start: 0.9069 (ptt180) cc_final: 0.8712 (ptt180) REVERT: W 74 LEU cc_start: 0.8401 (tp) cc_final: 0.7928 (pp) REVERT: W 75 THR cc_start: 0.7798 (p) cc_final: 0.7507 (p) REVERT: W 112 ASP cc_start: 0.8355 (m-30) cc_final: 0.7660 (p0) REVERT: W 153 GLU cc_start: 0.6939 (mt-10) cc_final: 0.5666 (mm-30) REVERT: W 162 HIS cc_start: 0.7325 (m170) cc_final: 0.6252 (m170) REVERT: W 290 TYR cc_start: 0.7412 (t80) cc_final: 0.7211 (t80) REVERT: Y 26 MET cc_start: 0.4167 (pmm) cc_final: 0.1945 (ppp) REVERT: Y 28 MET cc_start: 0.6680 (mmt) cc_final: 0.5908 (mmt) REVERT: Y 64 TYR cc_start: 0.8059 (p90) cc_final: 0.7602 (p90) REVERT: Y 129 ASP cc_start: 0.8858 (t70) cc_final: 0.8554 (t0) REVERT: Y 225 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8276 (tpp80) REVERT: Y 242 ARG cc_start: 0.8966 (ttt-90) cc_final: 0.8711 (ttp80) REVERT: Y 244 LYS cc_start: 0.8874 (tttt) cc_final: 0.8568 (tptp) REVERT: Y 268 TYR cc_start: 0.8008 (t80) cc_final: 0.7496 (t80) REVERT: D 67 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8833 (mm-30) REVERT: D 126 GLU cc_start: 0.8946 (pt0) cc_final: 0.8460 (pp20) REVERT: D 151 LYS cc_start: 0.9487 (ptmm) cc_final: 0.9046 (tppt) REVERT: D 162 HIS cc_start: 0.6928 (m170) cc_final: 0.6709 (m170) REVERT: D 180 ASN cc_start: 0.9364 (m-40) cc_final: 0.8795 (p0) REVERT: D 268 TYR cc_start: 0.8502 (t80) cc_final: 0.7937 (t80) REVERT: D 289 TRP cc_start: 0.8813 (m100) cc_final: 0.8411 (m100) REVERT: 0 109 ASN cc_start: 0.8485 (t0) cc_final: 0.8277 (t0) REVERT: 0 130 MET cc_start: 0.8869 (ttp) cc_final: 0.8545 (ttt) REVERT: 0 151 LYS cc_start: 0.9190 (pttm) cc_final: 0.8939 (mmtm) REVERT: 0 158 MET cc_start: 0.8278 (pmm) cc_final: 0.8063 (pmm) REVERT: 0 162 HIS cc_start: 0.7788 (m90) cc_final: 0.7322 (m170) REVERT: 0 180 ASN cc_start: 0.9288 (m110) cc_final: 0.9085 (m110) REVERT: 0 206 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8508 (mm-30) REVERT: 0 254 PHE cc_start: 0.9553 (m-80) cc_final: 0.9241 (m-80) REVERT: 0 268 TYR cc_start: 0.8619 (t80) cc_final: 0.8356 (t80) REVERT: 0 303 ASN cc_start: 0.9633 (m-40) cc_final: 0.9371 (t0) REVERT: 2 26 MET cc_start: 0.4200 (pmm) cc_final: 0.3212 (pmm) REVERT: 2 111 ASP cc_start: 0.7805 (m-30) cc_final: 0.7404 (m-30) REVERT: 2 162 HIS cc_start: 0.8105 (m90) cc_final: 0.7737 (m-70) REVERT: 2 303 ASN cc_start: 0.8639 (m110) cc_final: 0.8068 (t0) REVERT: 4 26 MET cc_start: 0.7109 (ptt) cc_final: 0.6310 (ptt) REVERT: 4 145 VAL cc_start: 0.7690 (t) cc_final: 0.7103 (t) REVERT: 4 201 MET cc_start: 0.1994 (pmm) cc_final: 0.0805 (ptm) outliers start: 1 outliers final: 0 residues processed: 636 average time/residue: 0.2732 time to fit residues: 271.8399 Evaluate side-chains 486 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 361 optimal weight: 6.9990 chunk 407 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 359 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 306 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 418 optimal weight: 6.9990 chunk 425 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN C 31 HIS C 183 ASN C 279 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 325 GLN H 123 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 172 GLN ** J 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN P 117 GLN P 162 HIS P 180 ASN P 279 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS R 212 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 325 GLN 0 279 GLN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 135 ASN 2 260 GLN 2 325 GLN 4 15 GLN ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.071172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.056929 restraints weight = 278516.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.058291 restraints weight = 209844.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.059320 restraints weight = 167167.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.060151 restraints weight = 139230.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.060787 restraints weight = 119197.000| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 1.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 41757 Z= 0.213 Angle : 0.833 17.161 56592 Z= 0.427 Chirality : 0.052 0.304 6512 Planarity : 0.007 0.226 7120 Dihedral : 20.491 179.318 6816 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % 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: -0.71 (0.11), residues: 5216 helix: 0.21 (0.11), residues: 2208 sheet: 0.10 (0.19), residues: 784 loop : -1.33 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG P 225 TYR 0.121 0.006 TYR P 102 PHE 0.034 0.002 PHE W 190 TRP 0.039 0.002 TRP L 289 HIS 0.007 0.002 HIS R 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (41712) covalent geometry : angle 0.83314 / 0.43 (56592) hydrogen bonds : bond 0.04118 / 2.79 ( 1904) hydrogen bonds : angle 5.71682 / 4.27 ( 5472) Misc. bond : bond 0.01108 / 0.72 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 605 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8892 (p90) cc_final: 0.8502 (p90) REVERT: A 91 PHE cc_start: 0.8540 (t80) cc_final: 0.8238 (t80) REVERT: A 130 MET cc_start: 0.8972 (ttt) cc_final: 0.8607 (ttt) REVERT: A 215 LYS cc_start: 0.9656 (ptpp) cc_final: 0.9363 (tmtt) REVERT: A 268 TYR cc_start: 0.8472 (t80) cc_final: 0.8218 (t80) REVERT: A 289 TRP cc_start: 0.8954 (m100) cc_final: 0.8348 (m100) REVERT: A 292 TYR cc_start: 0.9146 (t80) cc_final: 0.8682 (t80) REVERT: C 28 MET cc_start: 0.5530 (mmp) cc_final: 0.5326 (mmp) REVERT: C 112 ASP cc_start: 0.8974 (m-30) cc_final: 0.8457 (t0) REVERT: C 130 MET cc_start: 0.8844 (ptp) cc_final: 0.8503 (mmt) REVERT: C 138 ASP cc_start: 0.8250 (m-30) cc_final: 0.8031 (t0) REVERT: C 151 LYS cc_start: 0.9140 (pttt) cc_final: 0.8865 (tptt) REVERT: C 155 GLU cc_start: 0.8767 (pm20) cc_final: 0.7857 (pm20) REVERT: C 158 MET cc_start: 0.8535 (pmm) cc_final: 0.8118 (pmm) REVERT: C 217 TYR cc_start: 0.9125 (m-10) cc_final: 0.8809 (m-10) REVERT: F 113 LEU cc_start: 0.5915 (tp) cc_final: 0.5575 (tp) REVERT: F 135 ASN cc_start: 0.8542 (m-40) cc_final: 0.8310 (m110) REVERT: F 148 LEU cc_start: 0.8687 (mm) cc_final: 0.8479 (mm) REVERT: F 151 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7672 (mmmt) REVERT: F 254 PHE cc_start: 0.8529 (m-10) cc_final: 0.8074 (m-10) REVERT: F 314 ILE cc_start: 0.8156 (mm) cc_final: 0.7948 (mm) REVERT: H 26 MET cc_start: 0.4755 (ptt) cc_final: 0.4251 (ptm) REVERT: H 197 LYS cc_start: 0.8208 (mptt) cc_final: 0.7847 (mmtm) REVERT: H 242 ARG cc_start: 0.7418 (tpt90) cc_final: 0.6930 (tpt90) REVERT: H 314 ILE cc_start: 0.8991 (mt) cc_final: 0.8482 (mp) REVERT: J 64 TYR cc_start: 0.7362 (p90) cc_final: 0.7138 (p90) REVERT: J 158 MET cc_start: 0.8406 (mpp) cc_final: 0.8187 (mpp) REVERT: L 26 MET cc_start: 0.5203 (pmm) cc_final: 0.2920 (ptt) REVERT: L 126 GLU cc_start: 0.8739 (pt0) cc_final: 0.8327 (pp20) REVERT: L 158 MET cc_start: 0.8337 (mmp) cc_final: 0.7455 (mmp) REVERT: L 242 ARG cc_start: 0.8860 (ttt-90) cc_final: 0.8511 (ttp80) REVERT: N 18 ARG cc_start: 0.9242 (ptt-90) cc_final: 0.8985 (ptt180) REVERT: N 130 MET cc_start: 0.9015 (mtm) cc_final: 0.8485 (mtp) REVERT: N 151 LYS cc_start: 0.9380 (ptpp) cc_final: 0.9052 (pttm) REVERT: N 162 HIS cc_start: 0.7631 (m170) cc_final: 0.7275 (m170) REVERT: N 256 GLN cc_start: 0.8997 (pp30) cc_final: 0.8638 (pp30) REVERT: P 112 ASP cc_start: 0.8578 (t70) cc_final: 0.8262 (t0) REVERT: P 158 MET cc_start: 0.8375 (pmm) cc_final: 0.8011 (pmm) REVERT: P 262 LEU cc_start: 0.9091 (tt) cc_final: 0.8528 (tt) REVERT: P 265 LYS cc_start: 0.9212 (mptt) cc_final: 0.8644 (ttpt) REVERT: R 109 ASN cc_start: 0.8093 (t0) cc_final: 0.7751 (t0) REVERT: R 133 ARG cc_start: 0.8764 (ptp90) cc_final: 0.8490 (mtm110) REVERT: R 162 HIS cc_start: 0.8350 (m90) cc_final: 0.8122 (m170) REVERT: R 242 ARG cc_start: 0.8765 (pmt-80) cc_final: 0.8208 (tmm160) REVERT: U 13 LEU cc_start: 0.9137 (pp) cc_final: 0.8856 (pp) REVERT: U 148 LEU cc_start: 0.8246 (mt) cc_final: 0.7851 (mp) REVERT: U 162 HIS cc_start: 0.8533 (m90) cc_final: 0.8170 (m-70) REVERT: U 196 MET cc_start: 0.7309 (mmm) cc_final: 0.6376 (mmm) REVERT: U 223 ASP cc_start: 0.7472 (m-30) cc_final: 0.7168 (m-30) REVERT: U 225 ARG cc_start: 0.8577 (mtt-85) cc_final: 0.7908 (mtm-85) REVERT: W 5 LYS cc_start: 0.8944 (tmtt) cc_final: 0.8728 (tptt) REVERT: W 28 MET cc_start: 0.7774 (mmp) cc_final: 0.7471 (mmp) REVERT: W 153 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6489 (mm-30) REVERT: W 162 HIS cc_start: 0.7302 (m170) cc_final: 0.6387 (m170) REVERT: W 190 PHE cc_start: 0.6027 (t80) cc_final: 0.5701 (t80) REVERT: W 197 LYS cc_start: 0.9127 (mptt) cc_final: 0.8719 (mppt) REVERT: W 290 TYR cc_start: 0.7205 (t80) cc_final: 0.6979 (t80) REVERT: Y 26 MET cc_start: 0.4150 (pmm) cc_final: 0.2966 (pmm) REVERT: Y 64 TYR cc_start: 0.8247 (p90) cc_final: 0.7829 (p90) REVERT: Y 129 ASP cc_start: 0.8928 (t70) cc_final: 0.8563 (m-30) REVERT: Y 170 MET cc_start: 0.9234 (mmp) cc_final: 0.9000 (mmm) REVERT: Y 206 GLU cc_start: 0.9160 (mp0) cc_final: 0.8946 (mp0) REVERT: Y 225 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8186 (tpp80) REVERT: Y 268 TYR cc_start: 0.8017 (t80) cc_final: 0.7521 (t80) REVERT: D 67 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8752 (mm-30) REVERT: D 126 GLU cc_start: 0.9026 (pt0) cc_final: 0.8614 (pp20) REVERT: D 155 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8896 (mm-30) REVERT: D 180 ASN cc_start: 0.9323 (m-40) cc_final: 0.8778 (p0) REVERT: D 268 TYR cc_start: 0.8475 (t80) cc_final: 0.7971 (t80) REVERT: D 289 TRP cc_start: 0.8675 (m100) cc_final: 0.8300 (m100) REVERT: 0 105 LYS cc_start: 0.9335 (pttp) cc_final: 0.9003 (pttm) REVERT: 0 109 ASN cc_start: 0.8617 (t0) cc_final: 0.8406 (t0) REVERT: 0 151 LYS cc_start: 0.9252 (pttm) cc_final: 0.9021 (mmtt) REVERT: 0 158 MET cc_start: 0.8267 (pmm) cc_final: 0.8013 (pmm) REVERT: 0 162 HIS cc_start: 0.7776 (m90) cc_final: 0.7314 (m170) REVERT: 0 180 ASN cc_start: 0.9266 (m110) cc_final: 0.9062 (m110) REVERT: 0 206 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8559 (mm-30) REVERT: 0 254 PHE cc_start: 0.9586 (m-80) cc_final: 0.9316 (m-80) REVERT: 0 268 TYR cc_start: 0.8567 (t80) cc_final: 0.8309 (t80) REVERT: 0 303 ASN cc_start: 0.9621 (m-40) cc_final: 0.9392 (t0) REVERT: 2 26 MET cc_start: 0.4126 (pmm) cc_final: 0.3426 (pmm) REVERT: 2 111 ASP cc_start: 0.7888 (m-30) cc_final: 0.7567 (m-30) REVERT: 2 130 MET cc_start: 0.8847 (mmp) cc_final: 0.8600 (mmp) REVERT: 2 162 HIS cc_start: 0.8168 (m90) cc_final: 0.7834 (m-70) REVERT: 2 174 LEU cc_start: 0.8758 (mp) cc_final: 0.8177 (tt) REVERT: 2 303 ASN cc_start: 0.8712 (m110) cc_final: 0.8119 (t0) REVERT: 4 26 MET cc_start: 0.6618 (ptt) cc_final: 0.5860 (ptt) REVERT: 4 201 MET cc_start: 0.1667 (pmm) cc_final: 0.0804 (ptm) outliers start: 2 outliers final: 1 residues processed: 607 average time/residue: 0.2883 time to fit residues: 272.9483 Evaluate side-chains 473 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 371 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 465 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 416 optimal weight: 0.9990 chunk 328 optimal weight: 3.9990 chunk 343 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 447 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN A 325 GLN C 279 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN ** J 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN ** N 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN P 279 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN W 31 HIS W 180 ASN W 325 GLN ** Y 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 299 GLN Y 325 GLN D 162 HIS D 279 GLN D 325 GLN 0 279 GLN 2 117 GLN ** 2 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 180 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.074257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.059860 restraints weight = 252408.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.061220 restraints weight = 190926.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.062243 restraints weight = 152882.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.063071 restraints weight = 127824.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.063724 restraints weight = 110093.146| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 1.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41757 Z= 0.166 Angle : 0.800 11.996 56592 Z= 0.405 Chirality : 0.051 0.336 6512 Planarity : 0.006 0.078 7120 Dihedral : 20.392 177.671 6816 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.05 % Allowed : 1.00 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.11), residues: 5216 helix: 0.29 (0.11), residues: 2240 sheet: 0.27 (0.19), residues: 784 loop : -1.36 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG P 242 TYR 0.109 0.005 TYR P 102 PHE 0.027 0.002 PHE U 190 TRP 0.026 0.002 TRP J 289 HIS 0.017 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (41712) covalent geometry : angle 0.80039 / 0.41 (56592) hydrogen bonds : bond 0.03841 / 2.59 ( 1904) hydrogen bonds : angle 5.45795 / 4.08 ( 5472) Misc. bond : bond 0.01100 / 0.71 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 586 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.1720 (pmm) cc_final: 0.0470 (ppp) REVERT: A 64 TYR cc_start: 0.8798 (p90) cc_final: 0.8432 (p90) REVERT: A 91 PHE cc_start: 0.8573 (t80) cc_final: 0.8232 (t80) REVERT: A 130 MET cc_start: 0.8894 (ttt) cc_final: 0.8522 (ttt) REVERT: A 215 LYS cc_start: 0.9642 (ptpp) cc_final: 0.9316 (tmtt) REVERT: A 289 TRP cc_start: 0.8799 (m100) cc_final: 0.8212 (m100) REVERT: A 292 TYR cc_start: 0.9095 (t80) cc_final: 0.8561 (t80) REVERT: A 306 LYS cc_start: 0.9530 (ptpp) cc_final: 0.9316 (pttm) REVERT: C 28 MET cc_start: 0.5180 (mmp) cc_final: 0.4973 (mmp) REVERT: C 109 ASN cc_start: 0.8309 (t0) cc_final: 0.8079 (t0) REVERT: C 133 ARG cc_start: 0.9100 (mtm110) cc_final: 0.8762 (ptp-170) REVERT: C 138 ASP cc_start: 0.8309 (m-30) cc_final: 0.8032 (t70) REVERT: C 158 MET cc_start: 0.8466 (pmm) cc_final: 0.8225 (pmm) REVERT: F 127 ILE cc_start: 0.9613 (pt) cc_final: 0.9370 (pt) REVERT: F 254 PHE cc_start: 0.8245 (m-10) cc_final: 0.7781 (m-10) REVERT: F 314 ILE cc_start: 0.8029 (mm) cc_final: 0.7818 (mm) REVERT: H 26 MET cc_start: 0.4090 (ptt) cc_final: 0.3730 (ptm) REVERT: H 197 LYS cc_start: 0.8160 (mptt) cc_final: 0.7857 (mmtm) REVERT: H 242 ARG cc_start: 0.7399 (tpt90) cc_final: 0.6985 (tpt90) REVERT: J 28 MET cc_start: 0.8341 (mmm) cc_final: 0.8141 (mmm) REVERT: J 307 TYR cc_start: 0.8002 (m-80) cc_final: 0.7736 (m-10) REVERT: L 26 MET cc_start: 0.5145 (pmm) cc_final: 0.2885 (ptt) REVERT: L 126 GLU cc_start: 0.8739 (pt0) cc_final: 0.8390 (tp30) REVERT: L 242 ARG cc_start: 0.8890 (ttt-90) cc_final: 0.8403 (ttp80) REVERT: L 307 TYR cc_start: 0.9294 (t80) cc_final: 0.9086 (t80) REVERT: N 126 GLU cc_start: 0.8028 (pt0) cc_final: 0.7745 (pt0) REVERT: N 130 MET cc_start: 0.9146 (mtm) cc_final: 0.8595 (mtp) REVERT: N 151 LYS cc_start: 0.9356 (ptpp) cc_final: 0.9058 (pttm) REVERT: N 162 HIS cc_start: 0.7474 (m170) cc_final: 0.7113 (m170) REVERT: N 256 GLN cc_start: 0.8994 (pp30) cc_final: 0.8597 (pp30) REVERT: N 290 TYR cc_start: 0.9184 (m-80) cc_final: 0.8959 (m-10) REVERT: N 320 LYS cc_start: 0.9461 (ptpp) cc_final: 0.9174 (pttm) REVERT: P 111 ASP cc_start: 0.8133 (m-30) cc_final: 0.7846 (m-30) REVERT: P 112 ASP cc_start: 0.8495 (t70) cc_final: 0.8135 (t0) REVERT: P 158 MET cc_start: 0.8161 (pmm) cc_final: 0.7730 (pmm) REVERT: P 262 LEU cc_start: 0.9072 (tt) cc_final: 0.8814 (pt) REVERT: R 26 MET cc_start: 0.0825 (ptt) cc_final: 0.0520 (ptm) REVERT: R 109 ASN cc_start: 0.8104 (t0) cc_final: 0.7806 (t0) REVERT: R 162 HIS cc_start: 0.8386 (m90) cc_final: 0.8182 (m170) REVERT: R 242 ARG cc_start: 0.8769 (pmt-80) cc_final: 0.8242 (ttp80) REVERT: U 13 LEU cc_start: 0.9109 (pp) cc_final: 0.8854 (pp) REVERT: U 26 MET cc_start: 0.4723 (ptt) cc_final: 0.2985 (pmm) REVERT: U 148 LEU cc_start: 0.8187 (mt) cc_final: 0.7938 (mt) REVERT: U 162 HIS cc_start: 0.8387 (m90) cc_final: 0.8062 (m-70) REVERT: U 196 MET cc_start: 0.7310 (mmm) cc_final: 0.6417 (mmm) REVERT: U 223 ASP cc_start: 0.7537 (m-30) cc_final: 0.7184 (m-30) REVERT: U 225 ARG cc_start: 0.8522 (mtt-85) cc_final: 0.7846 (mtm-85) REVERT: W 5 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8680 (tptt) REVERT: W 7 ARG cc_start: 0.9093 (ptt180) cc_final: 0.8717 (ptt180) REVERT: W 112 ASP cc_start: 0.8455 (m-30) cc_final: 0.7864 (p0) REVERT: W 153 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6432 (mm-30) REVERT: W 162 HIS cc_start: 0.6932 (m170) cc_final: 0.6185 (m170) REVERT: W 163 VAL cc_start: 0.7349 (t) cc_final: 0.7084 (p) REVERT: W 190 PHE cc_start: 0.5797 (t80) cc_final: 0.5502 (t80) REVERT: W 197 LYS cc_start: 0.9100 (mptt) cc_final: 0.8720 (mppt) REVERT: W 290 TYR cc_start: 0.7249 (t80) cc_final: 0.7010 (t80) REVERT: Y 26 MET cc_start: 0.3479 (pmm) cc_final: 0.1312 (ptt) REVERT: Y 64 TYR cc_start: 0.8234 (p90) cc_final: 0.7742 (p90) REVERT: Y 129 ASP cc_start: 0.8871 (t70) cc_final: 0.8539 (t0) REVERT: Y 170 MET cc_start: 0.9263 (mmp) cc_final: 0.9032 (mmm) REVERT: Y 206 GLU cc_start: 0.9193 (mp0) cc_final: 0.8964 (mp0) REVERT: Y 242 ARG cc_start: 0.8893 (tmm160) cc_final: 0.8398 (ttp80) REVERT: Y 256 GLN cc_start: 0.8686 (pp30) cc_final: 0.8304 (pp30) REVERT: Y 268 TYR cc_start: 0.7876 (t80) cc_final: 0.7404 (t80) REVERT: D 67 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8711 (mm-30) REVERT: D 126 GLU cc_start: 0.9055 (pt0) cc_final: 0.8654 (pp20) REVERT: D 151 LYS cc_start: 0.9363 (ptmm) cc_final: 0.8944 (tppt) REVERT: D 162 HIS cc_start: 0.7137 (m90) cc_final: 0.6879 (m170) REVERT: D 180 ASN cc_start: 0.9282 (m-40) cc_final: 0.8727 (p0) REVERT: D 268 TYR cc_start: 0.8379 (t80) cc_final: 0.7932 (t80) REVERT: D 289 TRP cc_start: 0.8486 (m100) cc_final: 0.8129 (m100) REVERT: 0 109 ASN cc_start: 0.8610 (t0) cc_final: 0.8382 (t0) REVERT: 0 151 LYS cc_start: 0.9167 (pttm) cc_final: 0.8940 (mmmm) REVERT: 0 158 MET cc_start: 0.8137 (pmm) cc_final: 0.7871 (pmm) REVERT: 0 162 HIS cc_start: 0.7806 (m90) cc_final: 0.7382 (m170) REVERT: 0 254 PHE cc_start: 0.9538 (m-80) cc_final: 0.8909 (m-80) REVERT: 0 268 TYR cc_start: 0.8527 (t80) cc_final: 0.8294 (t80) REVERT: 2 26 MET cc_start: 0.3796 (pmm) cc_final: 0.2816 (pmm) REVERT: 2 111 ASP cc_start: 0.7865 (m-30) cc_final: 0.7571 (m-30) REVERT: 2 117 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: 2 148 LEU cc_start: 0.9107 (mm) cc_final: 0.8901 (mp) REVERT: 2 162 HIS cc_start: 0.8238 (m90) cc_final: 0.7910 (m-70) REVERT: 2 303 ASN cc_start: 0.8776 (m110) cc_final: 0.8197 (t0) REVERT: 4 26 MET cc_start: 0.6361 (ptt) cc_final: 0.5716 (ptt) REVERT: 4 201 MET cc_start: 0.1716 (pmm) cc_final: 0.0838 (ptm) outliers start: 2 outliers final: 1 residues processed: 588 average time/residue: 0.2669 time to fit residues: 246.7530 Evaluate side-chains 481 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 338 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 396 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 131 optimal weight: 0.4980 chunk 263 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN C 279 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 325 GLN H 123 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN ** J 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 325 GLN P 279 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 HIS ** W 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN ** Y 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 162 HIS Y 325 GLN D 325 GLN 0 279 GLN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 192 ASN 4 180 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.076858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.062369 restraints weight = 246107.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.063697 restraints weight = 187495.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.064677 restraints weight = 151282.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.065475 restraints weight = 127075.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.066051 restraints weight = 110590.886| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 1.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41757 Z= 0.158 Angle : 0.777 11.304 56592 Z= 0.394 Chirality : 0.049 0.284 6512 Planarity : 0.006 0.074 7120 Dihedral : 20.385 177.799 6816 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.02 % Allowed : 0.95 % Favored : 99.03 % 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 (0.11), residues: 5216 helix: 0.38 (0.11), residues: 2240 sheet: 0.33 (0.19), residues: 784 loop : -1.33 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 255 TYR 0.099 0.005 TYR L 102 PHE 0.020 0.002 PHE H 216 TRP 0.015 0.001 TRP J 289 HIS 0.015 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (41712) covalent geometry : angle 0.77719 / 0.39 (56592) hydrogen bonds : bond 0.03826 / 2.59 ( 1904) hydrogen bonds : angle 5.38799 / 4.03 ( 5472) Misc. bond : bond 0.01042 / 0.67 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8710.96 seconds wall clock time: 151 minutes 19.55 seconds (9079.55 seconds total)