Starting phenix.real_space_refine on Thu Mar 5 02:03:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a02_11591/03_2026/7a02_11591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a02_11591/03_2026/7a02_11591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a02_11591/03_2026/7a02_11591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a02_11591/03_2026/7a02_11591.map" model { file = "/net/cci-nas-00/data/ceres_data/7a02_11591/03_2026/7a02_11591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a02_11591/03_2026/7a02_11591.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 11776 2.51 5 N 2990 2.21 5 O 3818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18699 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W Time building chain proxies: 1.62, per 1000 atoms: 0.09 Number of scatterers: 18699 At special positions: 0 Unit cell: (108.976, 108.976, 141.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3818 8.00 N 2990 7.00 C 11776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS J 109 " distance=2.06 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS K 24 " distance=2.12 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS K 109 " distance=2.52 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS L 109 " distance=2.12 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS M 109 " distance=2.07 Simple disulfide: pdb=" SG CYS E 10 " - pdb=" SG CYS N 109 " distance=1.97 Simple disulfide: pdb=" SG CYS F 10 " - pdb=" SG CYS O 109 " distance=2.20 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS P 109 " distance=1.61 Simple disulfide: pdb=" SG CYS H 10 " - pdb=" SG CYS Q 109 " distance=1.93 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS R 109 " distance=1.93 Simple disulfide: pdb=" SG CYS J 10 " - pdb=" SG CYS S 109 " distance=1.91 Simple disulfide: pdb=" SG CYS K 10 " - pdb=" SG CYS W 109 " distance=1.94 Simple disulfide: pdb=" SG CYS L 10 " - pdb=" SG CYS T 109 " distance=2.06 Simple disulfide: pdb=" SG CYS M 10 " - pdb=" SG CYS V 109 " distance=2.26 Simple disulfide: pdb=" SG CYS N 10 " - pdb=" SG CYS U 109 " distance=1.96 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS L 24 " distance=1.77 Simple disulfide: pdb=" SG CYS C 11 " - pdb=" SG CYS M 24 " distance=1.97 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS N 24 " distance=2.17 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS O 24 " distance=2.08 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS P 24 " distance=2.22 Simple disulfide: pdb=" SG CYS G 11 " - pdb=" SG CYS Q 24 " distance=2.17 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS R 24 " distance=2.06 Simple disulfide: pdb=" SG CYS I 11 " - pdb=" SG CYS S 24 " distance=1.85 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS W 24 " distance=1.94 Simple disulfide: pdb=" SG CYS K 11 " - pdb=" SG CYS T 24 " distance=2.08 Simple disulfide: pdb=" SG CYS L 11 " - pdb=" SG CYS V 24 " distance=2.07 Simple disulfide: pdb=" SG CYS M 11 " - pdb=" SG CYS U 24 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 799.4 milliseconds 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4692 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.685A pdb=" N CYS A 10 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS K 24 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU K 104 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR K 105 " --> pdb=" O ASP K 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS K 52 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N SER K 84 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE L 36 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA L 38 " --> pdb=" O SER K 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR K 88 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL L 95 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU L 75 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER L 66 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU A 104 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 105 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 52 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N SER A 84 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE B 36 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 38 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 88 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 95 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER B 66 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 38 removed outlier: 6.562A pdb=" N VAL A 95 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 66 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.740A pdb=" N GLU L 104 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR L 105 " --> pdb=" O ASP L 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS L 52 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N SER L 84 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE M 36 " --> pdb=" O SER L 84 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA M 38 " --> pdb=" O SER L 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR L 88 " --> pdb=" O ALA M 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL M 95 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU M 75 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER M 66 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA M 73 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU B 104 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 105 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 52 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N SER B 84 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE C 36 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 38 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 88 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 95 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER C 66 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.690A pdb=" N CYS C 10 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS M 24 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU M 104 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR M 105 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS M 52 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N SER M 84 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE N 36 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA N 38 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR M 88 " --> pdb=" O ALA N 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL N 95 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU N 75 " --> pdb=" O PHE N 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER N 66 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA N 73 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU C 104 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 105 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 52 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 9.515A pdb=" N SER C 84 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE D 36 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL D 95 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER D 66 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.734A pdb=" N CYS D 10 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS N 24 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU N 104 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR N 105 " --> pdb=" O ASP N 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS N 52 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N SER N 84 " --> pdb=" O ALA O 34 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE O 36 " --> pdb=" O SER N 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL O 95 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU O 75 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER O 66 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA O 73 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU D 104 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR D 105 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 52 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N SER D 84 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE E 36 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 95 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER E 66 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.746A pdb=" N CYS E 10 " --> pdb=" O LYS O 22 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS O 24 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU O 104 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR O 105 " --> pdb=" O ASP O 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS O 52 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N SER O 84 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE P 36 " --> pdb=" O SER O 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER O 86 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA P 38 " --> pdb=" O SER O 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR O 88 " --> pdb=" O ALA P 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL P 95 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU P 75 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER P 66 " --> pdb=" O ALA P 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA P 73 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU E 104 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR E 105 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 52 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N SER E 84 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE F 36 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 38 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL F 95 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU F 75 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER F 66 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA F 73 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.795A pdb=" N CYS F 10 " --> pdb=" O LYS P 22 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS P 24 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU P 104 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR P 105 " --> pdb=" O ASP P 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS P 52 " --> pdb=" O GLU P 107 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N SER P 84 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE Q 36 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL Q 95 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU Q 75 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER Q 66 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA Q 73 " --> pdb=" O SER Q 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU F 104 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR F 105 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 52 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N SER F 84 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE G 36 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL G 95 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU G 75 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER G 66 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA G 73 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.896A pdb=" N CYS G 10 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS Q 24 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU Q 104 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR Q 105 " --> pdb=" O ASP Q 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Q 52 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N SER Q 84 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE R 36 " --> pdb=" O SER Q 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 38 " --> pdb=" O SER Q 86 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL R 95 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU R 75 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER R 66 " --> pdb=" O ALA R 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA R 73 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU G 104 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR G 105 " --> pdb=" O ASP G 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS G 52 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N SER G 84 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE H 36 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 95 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU H 75 " --> pdb=" O PHE H 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER H 66 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA H 73 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.754A pdb=" N CYS H 10 " --> pdb=" O LYS R 22 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS R 24 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU R 104 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR R 105 " --> pdb=" O ASP R 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 52 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N SER R 84 " --> pdb=" O ALA S 34 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE S 36 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL S 95 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU S 75 " --> pdb=" O PHE S 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER S 66 " --> pdb=" O ALA S 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA S 73 " --> pdb=" O SER S 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU H 104 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR H 105 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS H 52 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N SER H 84 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE I 36 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 95 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU I 75 " --> pdb=" O PHE I 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER I 66 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA I 73 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.689A pdb=" N CYS S 24 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU S 104 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR S 105 " --> pdb=" O ASP S 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS S 52 " --> pdb=" O GLU S 107 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N SER S 84 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE W 36 " --> pdb=" O SER S 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL W 95 " --> pdb=" O ILE W 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU W 75 " --> pdb=" O PHE W 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER W 66 " --> pdb=" O ALA W 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA W 73 " --> pdb=" O SER W 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU I 104 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR I 105 " --> pdb=" O ASP I 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS I 52 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N SER I 84 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE J 36 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL J 95 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU J 75 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER J 66 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA J 73 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.610A pdb=" N CYS J 10 " --> pdb=" O LYS W 22 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS W 24 " --> pdb=" O CYS J 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU W 104 " --> pdb=" O ALA W 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR W 105 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS W 52 " --> pdb=" O GLU W 107 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ALA T 34 " --> pdb=" O SER W 84 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N SER W 86 " --> pdb=" O ALA T 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE T 36 " --> pdb=" O SER W 86 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR W 88 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA T 38 " --> pdb=" O THR W 88 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ARG W 90 " --> pdb=" O ALA T 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL T 95 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU T 75 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER T 66 " --> pdb=" O ALA T 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA T 73 " --> pdb=" O SER T 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU J 104 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR J 105 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 52 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N SER J 84 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE K 36 " --> pdb=" O SER J 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL K 95 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU K 75 " --> pdb=" O PHE K 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER K 66 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA K 73 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.737A pdb=" N CYS K 10 " --> pdb=" O LYS T 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS T 24 " --> pdb=" O CYS K 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU T 104 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR T 105 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS T 52 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N SER T 84 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE V 36 " --> pdb=" O SER T 84 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR T 88 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL V 95 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU V 75 " --> pdb=" O PHE V 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER V 66 " --> pdb=" O ALA V 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA V 73 " --> pdb=" O SER V 66 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.696A pdb=" N CYS L 10 " --> pdb=" O LYS V 22 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS V 24 " --> pdb=" O CYS L 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU V 104 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR V 105 " --> pdb=" O ASP V 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS V 52 " --> pdb=" O GLU V 107 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N ALA U 34 " --> pdb=" O SER V 84 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N SER V 86 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE U 36 " --> pdb=" O SER V 86 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR V 88 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA U 38 " --> pdb=" O THR V 88 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ARG V 90 " --> pdb=" O ALA U 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL U 95 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU U 75 " --> pdb=" O PHE U 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER U 66 " --> pdb=" O ALA U 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA U 73 " --> pdb=" O SER U 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.635A pdb=" N CYS M 10 " --> pdb=" O LYS U 22 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS U 24 " --> pdb=" O CYS M 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU U 104 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR U 105 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS U 52 " --> pdb=" O GLU U 107 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5980 1.34 - 1.46: 4830 1.46 - 1.59: 8004 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 18952 Sorted by residual: bond pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.63e+00 bond pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CB CYS Q 24 " pdb=" SG CYS Q 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CB CYS M 24 " pdb=" SG CYS M 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CB CYS H 24 " pdb=" SG CYS H 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 18947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 22829 1.03 - 2.07: 2432 2.07 - 3.10: 484 3.10 - 4.13: 77 4.13 - 5.16: 76 Bond angle restraints: 25898 Sorted by residual: angle pdb=" CG ARG D 91 " pdb=" CD ARG D 91 " pdb=" NE ARG D 91 " ideal model delta sigma weight residual 112.00 117.16 -5.16 2.20e+00 2.07e-01 5.51e+00 angle pdb=" CG ARG S 91 " pdb=" CD ARG S 91 " pdb=" NE ARG S 91 " ideal model delta sigma weight residual 112.00 117.15 -5.15 2.20e+00 2.07e-01 5.48e+00 angle pdb=" CG ARG B 91 " pdb=" CD ARG B 91 " pdb=" NE ARG B 91 " ideal model delta sigma weight residual 112.00 117.15 -5.15 2.20e+00 2.07e-01 5.48e+00 angle pdb=" CG ARG K 91 " pdb=" CD ARG K 91 " pdb=" NE ARG K 91 " ideal model delta sigma weight residual 112.00 117.14 -5.14 2.20e+00 2.07e-01 5.47e+00 angle pdb=" CG ARG A 91 " pdb=" CD ARG A 91 " pdb=" NE ARG A 91 " ideal model delta sigma weight residual 112.00 117.14 -5.14 2.20e+00 2.07e-01 5.46e+00 ... (remaining 25893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 10298 17.02 - 34.04: 579 34.04 - 51.07: 92 51.07 - 68.09: 0 68.09 - 85.11: 60 Dihedral angle restraints: 11029 sinusoidal: 3669 harmonic: 7360 Sorted by residual: dihedral pdb=" CB CYS M 10 " pdb=" SG CYS M 10 " pdb=" SG CYS V 109 " pdb=" CB CYS V 109 " ideal model delta sinusoidal sigma weight residual 93.00 178.11 -85.11 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS B 10 " pdb=" SG CYS B 10 " pdb=" SG CYS K 109 " pdb=" CB CYS K 109 " ideal model delta sinusoidal sigma weight residual 93.00 178.06 -85.06 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS D 10 " pdb=" SG CYS D 10 " pdb=" SG CYS M 109 " pdb=" CB CYS M 109 " ideal model delta sinusoidal sigma weight residual 93.00 178.04 -85.04 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 11026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1752 0.032 - 0.065: 954 0.065 - 0.097: 299 0.097 - 0.130: 284 0.130 - 0.162: 46 Chirality restraints: 3335 Sorted by residual: chirality pdb=" CA CYS H 24 " pdb=" N CYS H 24 " pdb=" C CYS H 24 " pdb=" CB CYS H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA CYS J 24 " pdb=" N CYS J 24 " pdb=" C CYS J 24 " pdb=" CB CYS J 24 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA CYS S 24 " pdb=" N CYS S 24 " pdb=" C CYS S 24 " pdb=" CB CYS S 24 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 3332 not shown) Planarity restraints: 3197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 36 " -0.005 2.00e-02 2.50e+03 9.03e-03 8.16e-01 pdb=" C ILE P 36 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE P 36 " -0.006 2.00e-02 2.50e+03 pdb=" N TYR P 37 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 36 " 0.005 2.00e-02 2.50e+03 8.99e-03 8.08e-01 pdb=" C ILE H 36 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE H 36 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR H 37 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T 36 " 0.005 2.00e-02 2.50e+03 8.99e-03 8.08e-01 pdb=" C ILE T 36 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE T 36 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR T 37 " 0.005 2.00e-02 2.50e+03 ... (remaining 3194 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6732 2.84 - 3.35: 15398 3.35 - 3.87: 28208 3.87 - 4.38: 33474 4.38 - 4.90: 63111 Nonbonded interactions: 146923 Sorted by model distance: nonbonded pdb=" O SER C 117 " pdb=" OG SER C 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER U 117 " pdb=" OG SER U 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER H 117 " pdb=" OG SER H 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER D 117 " pdb=" OG SER D 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER M 117 " pdb=" OG SER M 117 " model vdw 2.324 3.040 ... (remaining 146918 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 14.860 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.010 0.493 18979 Z= 0.452 Angle : 0.802 17.027 25952 Z= 0.458 Chirality : 0.052 0.162 3335 Planarity : 0.002 0.009 3197 Dihedral : 12.609 83.656 6256 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: -0.20 (0.13), residues: 1357 loop : -2.69 (0.15), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.003 ARG J 90 TYR 0.009 0.002 TYR B 114 PHE 0.009 0.002 PHE U 108 TRP 0.002 0.001 TRP P 27 Details of bonding type rmsd covalent geometry : bond 0.00766 (18952) covalent geometry : angle 0.74023 (25898) SS BOND : bond 0.16883 ( 27) SS BOND : angle 6.82375 ( 54) hydrogen bonds : bond 0.15321 ( 944) hydrogen bonds : angle 6.91645 ( 2481) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 0.684 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: A 90 ARG cc_start: 0.8096 (ptt180) cc_final: 0.7879 (ptp90) REVERT: D 35 ILE cc_start: 0.8790 (mm) cc_final: 0.8559 (tp) REVERT: D 65 TYR cc_start: 0.8531 (m-80) cc_final: 0.8138 (m-80) REVERT: L 93 ASP cc_start: 0.7860 (t0) cc_final: 0.7659 (t0) REVERT: M 52 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8104 (tptp) REVERT: O 50 TYR cc_start: 0.8945 (p90) cc_final: 0.8626 (p90) REVERT: O 93 ASP cc_start: 0.7682 (t0) cc_final: 0.7481 (t0) REVERT: Q 93 ASP cc_start: 0.8112 (t0) cc_final: 0.7900 (t0) REVERT: R 22 LYS cc_start: 0.8541 (tttt) cc_final: 0.8284 (tttp) REVERT: W 52 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7992 (ttpp) REVERT: W 54 ASP cc_start: 0.8014 (t70) cc_final: 0.7647 (t70) REVERT: W 69 VAL cc_start: 0.9025 (p) cc_final: 0.8709 (t) outliers start: 0 outliers final: 1 residues processed: 665 average time/residue: 0.4056 time to fit residues: 318.5802 Evaluate side-chains 539 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 538 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 97 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110323 restraints weight = 24503.081| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.76 r_work: 0.3130 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18979 Z= 0.175 Angle : 0.640 10.804 25952 Z= 0.363 Chirality : 0.048 0.225 3335 Planarity : 0.003 0.030 3197 Dihedral : 4.852 20.199 2739 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.70 % Allowed : 14.39 % Favored : 80.91 % 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: -1.32 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.44 (0.13), residues: 1426 loop : -2.81 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 91 TYR 0.020 0.002 TYR D 50 PHE 0.014 0.002 PHE V 92 TRP 0.005 0.001 TRP T 27 Details of bonding type rmsd covalent geometry : bond 0.00421 (18952) covalent geometry : angle 0.61933 (25898) SS BOND : bond 0.00334 ( 27) SS BOND : angle 3.54914 ( 54) hydrogen bonds : bond 0.04431 ( 944) hydrogen bonds : angle 5.46579 ( 2481) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 595 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 CYS cc_start: 0.9192 (m) cc_final: 0.8907 (p) REVERT: A 42 SER cc_start: 0.8822 (t) cc_final: 0.8541 (m) REVERT: A 90 ARG cc_start: 0.8946 (ptt180) cc_final: 0.8642 (ppp80) REVERT: B 100 THR cc_start: 0.7871 (m) cc_final: 0.7348 (p) REVERT: C 84 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8974 (p) REVERT: E 90 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8459 (ptm-80) REVERT: E 91 ARG cc_start: 0.8900 (ptp-170) cc_final: 0.8624 (ptp-170) REVERT: G 21 ASP cc_start: 0.8565 (m-30) cc_final: 0.8313 (m-30) REVERT: H 46 TYR cc_start: 0.8867 (m-80) cc_final: 0.8495 (m-80) REVERT: H 93 ASP cc_start: 0.8024 (t0) cc_final: 0.7824 (t0) REVERT: I 69 VAL cc_start: 0.9193 (m) cc_final: 0.8952 (t) REVERT: I 77 ILE cc_start: 0.8028 (mt) cc_final: 0.7746 (mt) REVERT: J 24 CYS cc_start: 0.8870 (m) cc_final: 0.8668 (t) REVERT: K 93 ASP cc_start: 0.8696 (t0) cc_final: 0.8446 (t0) REVERT: P 52 LYS cc_start: 0.9310 (ptmm) cc_final: 0.9008 (ptmm) REVERT: Q 24 CYS cc_start: 0.8273 (m) cc_final: 0.7852 (m) REVERT: R 22 LYS cc_start: 0.9051 (tttt) cc_final: 0.8448 (tttp) REVERT: U 90 ARG cc_start: 0.8983 (ptt180) cc_final: 0.6888 (ptt-90) REVERT: U 98 LEU cc_start: 0.8812 (tp) cc_final: 0.8534 (tm) REVERT: W 10 CYS cc_start: 0.8409 (p) cc_final: 0.7635 (t) REVERT: W 107 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8567 (mt-10) outliers start: 94 outliers final: 63 residues processed: 629 average time/residue: 0.4387 time to fit residues: 323.2079 Evaluate side-chains 610 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 545 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 178 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109190 restraints weight = 24680.480| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.75 r_work: 0.3032 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18979 Z= 0.207 Angle : 0.638 11.160 25952 Z= 0.362 Chirality : 0.048 0.204 3335 Planarity : 0.003 0.047 3197 Dihedral : 4.903 20.359 2737 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 6.10 % Allowed : 19.34 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.53 (0.13), residues: 1426 loop : -2.88 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 91 TYR 0.022 0.002 TYR D 37 PHE 0.018 0.002 PHE V 92 TRP 0.005 0.001 TRP H 27 Details of bonding type rmsd covalent geometry : bond 0.00508 (18952) covalent geometry : angle 0.61818 (25898) SS BOND : bond 0.00472 ( 27) SS BOND : angle 3.47063 ( 54) hydrogen bonds : bond 0.04544 ( 944) hydrogen bonds : angle 5.43964 ( 2481) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 560 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 CYS cc_start: 0.9212 (m) cc_final: 0.8904 (p) REVERT: A 36 ILE cc_start: 0.8824 (tt) cc_final: 0.8579 (pt) REVERT: A 90 ARG cc_start: 0.8974 (ptt180) cc_final: 0.8513 (ppp80) REVERT: B 100 THR cc_start: 0.7926 (m) cc_final: 0.7517 (p) REVERT: C 84 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8990 (p) REVERT: F 91 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8462 (mtm-85) REVERT: G 21 ASP cc_start: 0.8629 (m-30) cc_final: 0.8387 (m-30) REVERT: H 46 TYR cc_start: 0.8920 (m-80) cc_final: 0.8694 (m-80) REVERT: H 91 ARG cc_start: 0.8380 (mtm180) cc_final: 0.8129 (ttm110) REVERT: H 93 ASP cc_start: 0.7930 (t0) cc_final: 0.7729 (t0) REVERT: J 24 CYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8719 (t) REVERT: K 93 ASP cc_start: 0.8650 (t0) cc_final: 0.8362 (t0) REVERT: L 90 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8071 (ptt90) REVERT: M 52 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8661 (ptmm) REVERT: O 105 THR cc_start: 0.8818 (t) cc_final: 0.8544 (p) REVERT: P 52 LYS cc_start: 0.9176 (ptmm) cc_final: 0.8887 (ptmm) REVERT: R 22 LYS cc_start: 0.9011 (tttt) cc_final: 0.8343 (tttp) REVERT: R 42 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8552 (t) REVERT: S 91 ARG cc_start: 0.8938 (mtm-85) cc_final: 0.8577 (mtm-85) REVERT: U 18 ILE cc_start: 0.8964 (mt) cc_final: 0.8670 (tt) REVERT: U 98 LEU cc_start: 0.8728 (tp) cc_final: 0.8446 (tm) REVERT: U 107 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7890 (mt-10) REVERT: W 10 CYS cc_start: 0.8272 (p) cc_final: 0.7632 (t) outliers start: 122 outliers final: 85 residues processed: 605 average time/residue: 0.4310 time to fit residues: 306.5917 Evaluate side-chains 620 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 530 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 54 ASP Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 201 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112489 restraints weight = 24425.021| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.74 r_work: 0.3066 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18979 Z= 0.158 Angle : 0.585 11.213 25952 Z= 0.334 Chirality : 0.047 0.223 3335 Planarity : 0.003 0.031 3197 Dihedral : 4.678 20.206 2737 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.40 % Allowed : 21.79 % Favored : 71.81 % 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: -1.17 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.67 (0.13), residues: 1426 loop : -2.91 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 91 TYR 0.018 0.002 TYR S 50 PHE 0.018 0.002 PHE T 64 TRP 0.005 0.001 TRP H 27 Details of bonding type rmsd covalent geometry : bond 0.00382 (18952) covalent geometry : angle 0.56975 (25898) SS BOND : bond 0.00599 ( 27) SS BOND : angle 3.00228 ( 54) hydrogen bonds : bond 0.03915 ( 944) hydrogen bonds : angle 5.30296 ( 2481) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 558 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 CYS cc_start: 0.9177 (m) cc_final: 0.8881 (p) REVERT: A 90 ARG cc_start: 0.9002 (ptt180) cc_final: 0.8541 (ppp80) REVERT: B 100 THR cc_start: 0.7907 (m) cc_final: 0.7567 (p) REVERT: C 36 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8148 (pt) REVERT: D 91 ARG cc_start: 0.9069 (mtm180) cc_final: 0.8796 (mtm180) REVERT: F 24 CYS cc_start: 0.8773 (t) cc_final: 0.8423 (p) REVERT: F 105 THR cc_start: 0.8658 (t) cc_final: 0.8428 (p) REVERT: G 21 ASP cc_start: 0.8623 (m-30) cc_final: 0.8418 (m-30) REVERT: H 91 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8109 (ttm110) REVERT: I 18 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8572 (pt) REVERT: J 24 CYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8803 (t) REVERT: K 93 ASP cc_start: 0.8660 (t0) cc_final: 0.8367 (t0) REVERT: M 52 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8648 (ptmm) REVERT: O 66 SER cc_start: 0.9172 (p) cc_final: 0.8941 (p) REVERT: O 105 THR cc_start: 0.8737 (t) cc_final: 0.8481 (p) REVERT: P 52 LYS cc_start: 0.9177 (ptmm) cc_final: 0.8914 (ptmm) REVERT: R 22 LYS cc_start: 0.9014 (tttt) cc_final: 0.8346 (tttp) REVERT: T 90 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8889 (ptt180) REVERT: T 98 LEU cc_start: 0.8526 (tp) cc_final: 0.8249 (tm) REVERT: U 18 ILE cc_start: 0.8946 (mt) cc_final: 0.8680 (tt) REVERT: U 90 ARG cc_start: 0.9002 (ptt180) cc_final: 0.6701 (ptt-90) REVERT: U 98 LEU cc_start: 0.8576 (tp) cc_final: 0.8341 (tm) REVERT: U 107 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7911 (mt-10) REVERT: W 10 CYS cc_start: 0.8257 (p) cc_final: 0.7723 (t) outliers start: 128 outliers final: 86 residues processed: 606 average time/residue: 0.4446 time to fit residues: 314.4428 Evaluate side-chains 623 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 531 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 ARG Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 110 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111927 restraints weight = 24176.654| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.74 r_work: 0.3052 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18979 Z= 0.191 Angle : 0.608 14.597 25952 Z= 0.346 Chirality : 0.047 0.239 3335 Planarity : 0.003 0.035 3197 Dihedral : 4.794 20.950 2737 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 7.85 % Allowed : 21.89 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.67 (0.13), residues: 1426 loop : -2.96 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 91 TYR 0.021 0.002 TYR E 65 PHE 0.020 0.002 PHE T 64 TRP 0.005 0.001 TRP B 27 Details of bonding type rmsd covalent geometry : bond 0.00467 (18952) covalent geometry : angle 0.59102 (25898) SS BOND : bond 0.00532 ( 27) SS BOND : angle 3.15757 ( 54) hydrogen bonds : bond 0.04184 ( 944) hydrogen bonds : angle 5.36439 ( 2481) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 536 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 CYS cc_start: 0.9201 (m) cc_final: 0.8891 (p) REVERT: A 90 ARG cc_start: 0.9042 (ptt180) cc_final: 0.8662 (ppp80) REVERT: A 113 ARG cc_start: 0.9035 (mtt-85) cc_final: 0.8778 (mtt90) REVERT: B 100 THR cc_start: 0.7923 (m) cc_final: 0.7623 (p) REVERT: C 36 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8091 (pt) REVERT: E 52 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8685 (ttmm) REVERT: E 54 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: F 105 THR cc_start: 0.8704 (t) cc_final: 0.8416 (p) REVERT: G 21 ASP cc_start: 0.8619 (m-30) cc_final: 0.8387 (m-30) REVERT: H 91 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8083 (ttm110) REVERT: I 18 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8603 (pt) REVERT: I 100 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7621 (p) REVERT: I 104 GLU cc_start: 0.8418 (mp0) cc_final: 0.8198 (mp0) REVERT: J 24 CYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8728 (t) REVERT: K 91 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8529 (tpp80) REVERT: K 93 ASP cc_start: 0.8641 (t0) cc_final: 0.8331 (t0) REVERT: L 90 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7951 (ptt90) REVERT: M 43 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8048 (mm-40) REVERT: M 52 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8668 (ptmm) REVERT: N 90 ARG cc_start: 0.9187 (ptt90) cc_final: 0.8972 (ptt180) REVERT: O 66 SER cc_start: 0.9175 (p) cc_final: 0.8941 (p) REVERT: O 105 THR cc_start: 0.8775 (t) cc_final: 0.8547 (p) REVERT: P 52 LYS cc_start: 0.9181 (ptmm) cc_final: 0.8914 (ptmm) REVERT: P 90 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8399 (ptt180) REVERT: P 91 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8507 (mtp85) REVERT: Q 91 ARG cc_start: 0.8718 (ttm110) cc_final: 0.7914 (mtm-85) REVERT: R 22 LYS cc_start: 0.9029 (tttt) cc_final: 0.8341 (tttp) REVERT: T 90 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8898 (ptt180) REVERT: T 98 LEU cc_start: 0.8549 (tp) cc_final: 0.8270 (tm) REVERT: U 18 ILE cc_start: 0.8960 (mt) cc_final: 0.8709 (tt) REVERT: U 98 LEU cc_start: 0.8604 (tp) cc_final: 0.8339 (tm) REVERT: U 107 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7932 (mt-10) REVERT: V 98 LEU cc_start: 0.8316 (tp) cc_final: 0.7931 (tm) REVERT: W 10 CYS cc_start: 0.8097 (p) cc_final: 0.7635 (t) outliers start: 157 outliers final: 106 residues processed: 599 average time/residue: 0.4203 time to fit residues: 296.4522 Evaluate side-chains 638 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 518 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 91 ARG Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 24 CYS Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 ARG Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 250 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110414 restraints weight = 24281.575| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.73 r_work: 0.3046 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18979 Z= 0.190 Angle : 0.604 12.363 25952 Z= 0.344 Chirality : 0.047 0.227 3335 Planarity : 0.003 0.037 3197 Dihedral : 4.815 21.310 2737 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 8.45 % Allowed : 21.49 % Favored : 70.06 % 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: -1.20 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.68 (0.13), residues: 1426 loop : -3.00 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 91 TYR 0.015 0.002 TYR I 114 PHE 0.020 0.002 PHE T 64 TRP 0.005 0.001 TRP B 27 Details of bonding type rmsd covalent geometry : bond 0.00464 (18952) covalent geometry : angle 0.59043 (25898) SS BOND : bond 0.00553 ( 27) SS BOND : angle 2.87498 ( 54) hydrogen bonds : bond 0.04138 ( 944) hydrogen bonds : angle 5.33382 ( 2481) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 535 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 CYS cc_start: 0.9193 (m) cc_final: 0.8890 (p) REVERT: A 90 ARG cc_start: 0.9028 (ptt180) cc_final: 0.8625 (ppp80) REVERT: A 113 ARG cc_start: 0.9035 (mtt-85) cc_final: 0.8779 (mtt90) REVERT: B 100 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7615 (p) REVERT: C 36 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8077 (pt) REVERT: C 88 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8132 (p) REVERT: E 52 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8706 (ttmm) REVERT: F 24 CYS cc_start: 0.8896 (t) cc_final: 0.8350 (p) REVERT: F 105 THR cc_start: 0.8680 (t) cc_final: 0.8402 (p) REVERT: F 107 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8397 (mt-10) REVERT: G 21 ASP cc_start: 0.8634 (m-30) cc_final: 0.8414 (m-30) REVERT: H 91 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8085 (ttm110) REVERT: I 18 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8610 (pt) REVERT: I 100 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7591 (p) REVERT: I 104 GLU cc_start: 0.8438 (mp0) cc_final: 0.8200 (mp0) REVERT: J 24 CYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8725 (t) REVERT: K 91 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8632 (tpp80) REVERT: L 90 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7971 (ptt90) REVERT: M 43 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7997 (mm-40) REVERT: M 52 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8663 (ptmm) REVERT: N 90 ARG cc_start: 0.9203 (ptt90) cc_final: 0.8990 (ptt180) REVERT: O 66 SER cc_start: 0.9172 (p) cc_final: 0.8937 (p) REVERT: O 105 THR cc_start: 0.8761 (t) cc_final: 0.8543 (p) REVERT: P 52 LYS cc_start: 0.9169 (ptmm) cc_final: 0.8908 (ptmm) REVERT: P 90 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8397 (ptt180) REVERT: P 91 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8524 (mtp85) REVERT: Q 91 ARG cc_start: 0.8690 (ttm110) cc_final: 0.7857 (mtm-85) REVERT: R 22 LYS cc_start: 0.9022 (tttt) cc_final: 0.8329 (tttp) REVERT: T 90 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8891 (ptt180) REVERT: T 98 LEU cc_start: 0.8550 (tp) cc_final: 0.8277 (tm) REVERT: U 18 ILE cc_start: 0.8953 (mt) cc_final: 0.8709 (tt) REVERT: U 98 LEU cc_start: 0.8625 (tp) cc_final: 0.8341 (tm) REVERT: U 107 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7922 (mt-10) REVERT: V 98 LEU cc_start: 0.8307 (tp) cc_final: 0.7910 (tm) REVERT: W 10 CYS cc_start: 0.8110 (p) cc_final: 0.7706 (t) REVERT: W 91 ARG cc_start: 0.9034 (ttm110) cc_final: 0.8830 (ttm110) outliers start: 169 outliers final: 124 residues processed: 613 average time/residue: 0.4065 time to fit residues: 293.9837 Evaluate side-chains 665 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 526 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 91 ARG Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 52 LYS Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 24 CYS Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 ARG Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110339 restraints weight = 24372.474| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.75 r_work: 0.3073 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18979 Z= 0.186 Angle : 0.600 10.256 25952 Z= 0.342 Chirality : 0.047 0.265 3335 Planarity : 0.003 0.039 3197 Dihedral : 4.800 21.403 2737 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 8.30 % Allowed : 22.49 % Favored : 69.22 % 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: -1.20 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.70 (0.13), residues: 1426 loop : -3.02 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 91 TYR 0.025 0.002 TYR E 65 PHE 0.020 0.002 PHE T 64 TRP 0.005 0.001 TRP B 27 Details of bonding type rmsd covalent geometry : bond 0.00453 (18952) covalent geometry : angle 0.58579 (25898) SS BOND : bond 0.00559 ( 27) SS BOND : angle 2.90430 ( 54) hydrogen bonds : bond 0.04078 ( 944) hydrogen bonds : angle 5.31991 ( 2481) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 534 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 CYS cc_start: 0.9177 (m) cc_final: 0.8912 (p) REVERT: A 66 SER cc_start: 0.9194 (p) cc_final: 0.8903 (p) REVERT: A 90 ARG cc_start: 0.9037 (ptt180) cc_final: 0.8670 (ppp80) REVERT: B 100 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7793 (p) REVERT: C 36 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8152 (pt) REVERT: D 91 ARG cc_start: 0.9055 (mtm180) cc_final: 0.8622 (mtm180) REVERT: D 114 TYR cc_start: 0.8954 (p90) cc_final: 0.8690 (p90) REVERT: E 52 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8751 (ttmm) REVERT: E 54 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: F 24 CYS cc_start: 0.8885 (t) cc_final: 0.8388 (p) REVERT: F 105 THR cc_start: 0.8734 (t) cc_final: 0.8470 (p) REVERT: G 21 ASP cc_start: 0.8636 (m-30) cc_final: 0.8436 (m-30) REVERT: G 52 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8726 (ptmm) REVERT: I 18 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8631 (pt) REVERT: I 100 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7694 (p) REVERT: I 104 GLU cc_start: 0.8495 (mp0) cc_final: 0.8141 (mp0) REVERT: J 24 CYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8745 (t) REVERT: K 93 ASP cc_start: 0.8749 (t0) cc_final: 0.8338 (t0) REVERT: L 90 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8007 (ptt90) REVERT: M 43 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8153 (mm-40) REVERT: M 52 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8729 (ptmm) REVERT: N 90 ARG cc_start: 0.9244 (ptt90) cc_final: 0.9028 (ptt180) REVERT: O 66 SER cc_start: 0.9222 (p) cc_final: 0.9004 (p) REVERT: P 52 LYS cc_start: 0.9226 (ptmm) cc_final: 0.8974 (ptmm) REVERT: P 90 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8444 (ptt180) REVERT: P 91 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8515 (mtp85) REVERT: Q 91 ARG cc_start: 0.8686 (ttm110) cc_final: 0.7929 (mtm-85) REVERT: R 21 ASP cc_start: 0.8707 (m-30) cc_final: 0.8473 (m-30) REVERT: R 22 LYS cc_start: 0.9062 (tttt) cc_final: 0.8410 (tttp) REVERT: T 90 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8934 (ptt180) REVERT: T 98 LEU cc_start: 0.8621 (tp) cc_final: 0.8372 (tm) REVERT: U 18 ILE cc_start: 0.9000 (mt) cc_final: 0.8774 (tt) REVERT: U 98 LEU cc_start: 0.8707 (tp) cc_final: 0.8436 (tm) REVERT: U 107 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7932 (mt-10) REVERT: V 90 ARG cc_start: 0.9034 (ptt180) cc_final: 0.8699 (ptt90) REVERT: V 98 LEU cc_start: 0.8333 (tp) cc_final: 0.8002 (tm) REVERT: W 10 CYS cc_start: 0.8133 (p) cc_final: 0.7689 (t) outliers start: 166 outliers final: 133 residues processed: 609 average time/residue: 0.4147 time to fit residues: 297.0065 Evaluate side-chains 664 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 518 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 52 LYS Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 24 CYS Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 ARG Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 3 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 133 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108238 restraints weight = 24609.955| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.75 r_work: 0.3033 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18979 Z= 0.230 Angle : 0.650 10.349 25952 Z= 0.368 Chirality : 0.048 0.260 3335 Planarity : 0.003 0.045 3197 Dihedral : 5.009 22.314 2737 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 8.45 % Allowed : 22.34 % Favored : 69.22 % 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: -1.42 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.58 (0.13), residues: 1334 loop : -2.93 (0.13), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 91 TYR 0.038 0.002 TYR K 37 PHE 0.022 0.002 PHE T 64 TRP 0.006 0.001 TRP B 27 Details of bonding type rmsd covalent geometry : bond 0.00561 (18952) covalent geometry : angle 0.63340 (25898) SS BOND : bond 0.00543 ( 27) SS BOND : angle 3.23834 ( 54) hydrogen bonds : bond 0.04502 ( 944) hydrogen bonds : angle 5.40949 ( 2481) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 529 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 CYS cc_start: 0.9196 (m) cc_final: 0.8916 (p) REVERT: A 90 ARG cc_start: 0.9064 (ptt180) cc_final: 0.8677 (ppp80) REVERT: B 100 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7793 (p) REVERT: D 91 ARG cc_start: 0.9070 (mtm180) cc_final: 0.8784 (mtm180) REVERT: D 114 TYR cc_start: 0.8969 (p90) cc_final: 0.8690 (p90) REVERT: E 52 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8760 (ttmm) REVERT: E 54 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: F 105 THR cc_start: 0.8741 (t) cc_final: 0.8508 (p) REVERT: G 21 ASP cc_start: 0.8642 (m-30) cc_final: 0.8435 (m-30) REVERT: I 18 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8650 (pt) REVERT: I 100 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7742 (p) REVERT: I 104 GLU cc_start: 0.8575 (mp0) cc_final: 0.8336 (mp0) REVERT: J 24 CYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8723 (t) REVERT: K 21 ASP cc_start: 0.8344 (m-30) cc_final: 0.8117 (m-30) REVERT: L 90 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8014 (ptt90) REVERT: M 43 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8162 (mm-40) REVERT: M 52 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8759 (ptmm) REVERT: N 90 ARG cc_start: 0.9248 (ptt90) cc_final: 0.9035 (ptt180) REVERT: O 66 SER cc_start: 0.9236 (p) cc_final: 0.9022 (p) REVERT: P 52 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8986 (ptmm) REVERT: P 90 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8490 (ptt180) REVERT: P 91 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8292 (mtp85) REVERT: Q 91 ARG cc_start: 0.8680 (ttm110) cc_final: 0.7936 (mtm-85) REVERT: R 21 ASP cc_start: 0.8696 (m-30) cc_final: 0.8448 (m-30) REVERT: R 22 LYS cc_start: 0.9072 (tttt) cc_final: 0.8397 (tttp) REVERT: T 90 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8957 (ptt180) REVERT: T 98 LEU cc_start: 0.8633 (tp) cc_final: 0.8377 (tm) REVERT: U 18 ILE cc_start: 0.9030 (mt) cc_final: 0.8794 (tt) REVERT: U 107 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7979 (mt-10) REVERT: V 90 ARG cc_start: 0.9046 (ptt180) cc_final: 0.8683 (ptt90) REVERT: V 98 LEU cc_start: 0.8344 (tp) cc_final: 0.7970 (tm) REVERT: W 10 CYS cc_start: 0.8063 (p) cc_final: 0.7689 (t) REVERT: W 91 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8900 (ttm110) outliers start: 169 outliers final: 132 residues processed: 608 average time/residue: 0.4212 time to fit residues: 300.4368 Evaluate side-chains 663 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 519 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 52 LYS Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 24 CYS Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 ARG Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 24 CYS Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 72 optimal weight: 8.9990 chunk 68 optimal weight: 0.0050 chunk 188 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 243 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 overall best weight: 4.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110913 restraints weight = 24479.291| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.76 r_work: 0.3154 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18979 Z= 0.140 Angle : 0.578 9.968 25952 Z= 0.329 Chirality : 0.046 0.254 3335 Planarity : 0.003 0.043 3197 Dihedral : 4.622 20.462 2737 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 7.50 % Allowed : 23.24 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.76 (0.13), residues: 1426 loop : -3.02 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 91 TYR 0.036 0.002 TYR E 65 PHE 0.019 0.001 PHE T 64 TRP 0.005 0.001 TRP H 27 Details of bonding type rmsd covalent geometry : bond 0.00336 (18952) covalent geometry : angle 0.56433 (25898) SS BOND : bond 0.00453 ( 27) SS BOND : angle 2.80284 ( 54) hydrogen bonds : bond 0.03593 ( 944) hydrogen bonds : angle 5.18670 ( 2481) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 544 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.9023 (ptt180) cc_final: 0.8733 (ppp80) REVERT: A 105 THR cc_start: 0.8793 (t) cc_final: 0.8592 (m) REVERT: B 100 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7861 (p) REVERT: D 91 ARG cc_start: 0.9004 (mtm180) cc_final: 0.8641 (mtm180) REVERT: D 114 TYR cc_start: 0.8965 (p90) cc_final: 0.8695 (p90) REVERT: E 52 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8700 (ttmm) REVERT: E 54 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: F 24 CYS cc_start: 0.8754 (t) cc_final: 0.8415 (p) REVERT: F 52 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8779 (pttm) REVERT: F 105 THR cc_start: 0.8700 (t) cc_final: 0.8439 (p) REVERT: G 21 ASP cc_start: 0.8701 (m-30) cc_final: 0.8457 (m-30) REVERT: G 52 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8715 (ptmm) REVERT: I 18 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8646 (pt) REVERT: I 100 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7733 (p) REVERT: K 93 ASP cc_start: 0.8707 (t0) cc_final: 0.8370 (t0) REVERT: L 90 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8030 (ptt90) REVERT: M 43 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8025 (mm-40) REVERT: M 52 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8792 (ptmm) REVERT: N 72 THR cc_start: 0.8649 (m) cc_final: 0.8394 (p) REVERT: P 52 LYS cc_start: 0.9265 (ptmm) cc_final: 0.9025 (ptmm) REVERT: P 90 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8484 (ptt180) REVERT: P 91 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8494 (mtp85) REVERT: Q 91 ARG cc_start: 0.8642 (ttm110) cc_final: 0.7896 (mtm-85) REVERT: R 21 ASP cc_start: 0.8696 (m-30) cc_final: 0.8487 (m-30) REVERT: R 22 LYS cc_start: 0.9062 (tttt) cc_final: 0.8462 (tttp) REVERT: T 98 LEU cc_start: 0.8703 (tp) cc_final: 0.8486 (tm) REVERT: U 90 ARG cc_start: 0.9059 (ptt180) cc_final: 0.6877 (ptt-90) REVERT: U 107 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8017 (mt-10) REVERT: V 90 ARG cc_start: 0.9011 (ptt180) cc_final: 0.8723 (ptt90) REVERT: V 98 LEU cc_start: 0.8391 (tp) cc_final: 0.8101 (tm) REVERT: W 10 CYS cc_start: 0.8060 (p) cc_final: 0.7628 (t) REVERT: W 91 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8912 (ttm110) outliers start: 150 outliers final: 113 residues processed: 617 average time/residue: 0.4298 time to fit residues: 311.5548 Evaluate side-chains 647 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 524 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 24 CYS Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 52 LYS Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 24 CYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 85 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 218 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 145 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108011 restraints weight = 24550.710| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.66 r_work: 0.3088 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18979 Z= 0.249 Angle : 0.675 12.013 25952 Z= 0.381 Chirality : 0.049 0.298 3335 Planarity : 0.003 0.050 3197 Dihedral : 5.064 22.436 2737 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.50 % Allowed : 24.34 % Favored : 69.17 % 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: -1.24 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.68 (0.13), residues: 1426 loop : -3.07 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 91 TYR 0.026 0.002 TYR P 50 PHE 0.024 0.002 PHE T 64 TRP 0.007 0.001 TRP R 27 Details of bonding type rmsd covalent geometry : bond 0.00611 (18952) covalent geometry : angle 0.65690 (25898) SS BOND : bond 0.00681 ( 27) SS BOND : angle 3.45648 ( 54) hydrogen bonds : bond 0.04602 ( 944) hydrogen bonds : angle 5.40984 ( 2481) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 532 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.9073 (ptt180) cc_final: 0.8744 (ppp80) REVERT: C 50 TYR cc_start: 0.9016 (p90) cc_final: 0.8810 (p90) REVERT: D 114 TYR cc_start: 0.9001 (p90) cc_final: 0.8750 (p90) REVERT: E 52 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8800 (ttmm) REVERT: E 54 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: F 52 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8862 (pttm) REVERT: F 105 THR cc_start: 0.8767 (t) cc_final: 0.8530 (p) REVERT: G 52 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8787 (ptmm) REVERT: I 18 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8675 (pt) REVERT: I 57 THR cc_start: 0.8729 (t) cc_final: 0.8511 (t) REVERT: I 100 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7861 (p) REVERT: L 90 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8039 (ptt90) REVERT: M 43 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8182 (mm-40) REVERT: M 52 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8831 (ptmm) REVERT: N 72 THR cc_start: 0.8710 (m) cc_final: 0.8436 (p) REVERT: O 113 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8658 (mtt90) REVERT: P 9 SER cc_start: 0.8424 (p) cc_final: 0.8171 (p) REVERT: P 52 LYS cc_start: 0.9290 (ptmm) cc_final: 0.9040 (ptmm) REVERT: P 90 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8506 (ptt180) REVERT: P 91 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8303 (mtp85) REVERT: Q 91 ARG cc_start: 0.8647 (ttm110) cc_final: 0.7985 (mtm-85) REVERT: R 22 LYS cc_start: 0.9122 (tttt) cc_final: 0.8477 (tttp) REVERT: T 98 LEU cc_start: 0.8728 (tp) cc_final: 0.8499 (tm) REVERT: U 107 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8105 (mt-10) REVERT: V 90 ARG cc_start: 0.9069 (ptt180) cc_final: 0.8764 (ptt90) REVERT: V 98 LEU cc_start: 0.8396 (tp) cc_final: 0.8051 (tm) REVERT: W 10 CYS cc_start: 0.8031 (p) cc_final: 0.7618 (t) REVERT: W 91 ARG cc_start: 0.9137 (ttm110) cc_final: 0.8898 (ttm110) outliers start: 130 outliers final: 109 residues processed: 593 average time/residue: 0.4482 time to fit residues: 311.1771 Evaluate side-chains 642 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 524 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 52 LYS Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 24 CYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 33 optimal weight: 30.0000 chunk 209 optimal weight: 50.0000 chunk 77 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106904 restraints weight = 24977.758| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.68 r_work: 0.3141 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 18979 Z= 0.268 Angle : 0.700 12.202 25952 Z= 0.394 Chirality : 0.050 0.289 3335 Planarity : 0.004 0.051 3197 Dihedral : 5.202 22.942 2737 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 6.70 % Allowed : 24.44 % Favored : 68.87 % 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: -1.34 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.61 (0.13), residues: 1426 loop : -3.13 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 91 TYR 0.028 0.002 TYR K 37 PHE 0.024 0.002 PHE T 64 TRP 0.007 0.001 TRP R 27 Details of bonding type rmsd covalent geometry : bond 0.00659 (18952) covalent geometry : angle 0.68045 (25898) SS BOND : bond 0.00733 ( 27) SS BOND : angle 3.68871 ( 54) hydrogen bonds : bond 0.04783 ( 944) hydrogen bonds : angle 5.44015 ( 2481) =============================================================================== Job complete usr+sys time: 6759.48 seconds wall clock time: 115 minutes 55.79 seconds (6955.79 seconds total)