Starting phenix.real_space_refine on Thu Mar 5 15:18:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tsv_10566/03_2026/6tsv_10566.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tsv_10566/03_2026/6tsv_10566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tsv_10566/03_2026/6tsv_10566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tsv_10566/03_2026/6tsv_10566.map" model { file = "/net/cci-nas-00/data/ceres_data/6tsv_10566/03_2026/6tsv_10566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tsv_10566/03_2026/6tsv_10566.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 48 5.16 5 C 14952 2.51 5 N 4008 2.21 5 O 4824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 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: 23832 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Restraints were copied for chains: A, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 2.07, per 1000 atoms: 0.09 Number of scatterers: 23832 At special positions: 0 Unit cell: (100.985, 100.985, 173.269, 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 48 16.00 O 4824 8.00 N 4008 7.00 C 14952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 13.4% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP B 8 " --> pdb=" O ASN B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP A 8 " --> pdb=" O ASN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP C 8 " --> pdb=" O ASN C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 84 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP D 8 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP E 8 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 84 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP F 8 " --> pdb=" O ASN F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE F 82 " --> pdb=" O ARG F 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE F 84 " --> pdb=" O ARG F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP G 8 " --> pdb=" O ASN G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP H 8 " --> pdb=" O ASN H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 removed outlier: 3.669A pdb=" N ASP I 8 " --> pdb=" O ASN I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE I 83 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP J 8 " --> pdb=" O ASN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE J 82 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE J 83 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP K 8 " --> pdb=" O ASN K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP M 8 " --> pdb=" O ASN M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP N 8 " --> pdb=" O ASN N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP O 8 " --> pdb=" O ASN O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE O 82 " --> pdb=" O ARG O 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE O 84 " --> pdb=" O ARG O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP P 8 " --> pdb=" O ASN P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE P 82 " --> pdb=" O ARG P 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE P 83 " --> pdb=" O ALA P 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 84 " --> pdb=" O ARG P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP R 8 " --> pdb=" O ASN R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE R 82 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 84 " --> pdb=" O ARG R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP S 8 " --> pdb=" O ASN S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE S 82 " --> pdb=" O ARG S 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE S 83 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP T 8 " --> pdb=" O ASN T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE T 83 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE T 84 " --> pdb=" O ARG T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.669A pdb=" N ASP U 8 " --> pdb=" O ASN U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE U 82 " --> pdb=" O ARG U 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE U 83 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE U 84 " --> pdb=" O ARG U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP V 8 " --> pdb=" O ASN V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE V 82 " --> pdb=" O ARG V 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE V 84 " --> pdb=" O ARG V 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP W 8 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE W 82 " --> pdb=" O ARG W 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE W 83 " --> pdb=" O ALA W 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE W 84 " --> pdb=" O ARG W 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP X 8 " --> pdb=" O ASN X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE X 82 " --> pdb=" O ARG X 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE X 83 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE X 84 " --> pdb=" O ARG X 80 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP B 14 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 90 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 107 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 127 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA B 62 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 69 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU B 27 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP B 14 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 90 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP A 14 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU A 90 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE A 107 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 127 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 62 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 69 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 27 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP A 14 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU A 90 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP C 14 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU C 90 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 107 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 127 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA C 62 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 69 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU C 27 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP C 14 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU C 90 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP D 14 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU D 90 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE D 107 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA D 62 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL D 69 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU D 27 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP D 14 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU D 90 " --> pdb=" O ASP D 14 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP E 14 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU E 90 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE E 107 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA E 127 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA E 62 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL E 69 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU E 27 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP E 14 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU E 90 " --> pdb=" O ASP E 14 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP F 14 " --> pdb=" O GLU F 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU F 90 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE F 107 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA F 127 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA F 62 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL F 69 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU F 27 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP F 14 " --> pdb=" O GLU F 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU F 90 " --> pdb=" O ASP F 14 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP G 14 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU G 90 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL G 69 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU G 27 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP G 14 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU G 90 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP H 14 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU H 90 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE H 107 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA H 127 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA H 62 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL H 69 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU H 27 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP H 14 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU H 90 " --> pdb=" O ASP H 14 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'I' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP I 14 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU I 90 " --> pdb=" O ASP I 14 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE I 107 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA I 127 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA I 62 " --> pdb=" O SER I 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 69 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU I 27 " --> pdb=" O VAL I 69 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP I 14 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU I 90 " --> pdb=" O ASP I 14 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'J' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP J 14 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU J 90 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE J 107 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA J 127 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA J 62 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL J 69 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU J 27 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'J' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP J 14 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU J 90 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP K 14 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU K 90 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE K 107 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA K 127 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA K 62 " --> pdb=" O SER K 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL K 69 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU K 27 " --> pdb=" O VAL K 69 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP K 14 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU K 90 " --> pdb=" O ASP K 14 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP L 14 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU L 90 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE L 107 " --> pdb=" O ALA L 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA L 127 " --> pdb=" O ILE L 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA L 62 " --> pdb=" O SER L 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL L 69 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU L 27 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP L 14 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU L 90 " --> pdb=" O ASP L 14 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'M' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP M 14 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU M 90 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE M 107 " --> pdb=" O ALA M 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA M 127 " --> pdb=" O ILE M 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA M 62 " --> pdb=" O SER M 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL M 69 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU M 27 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'M' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP M 14 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU M 90 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'N' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP N 14 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU N 90 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL N 69 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU N 27 " --> pdb=" O VAL N 69 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'N' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP N 14 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU N 90 " --> pdb=" O ASP N 14 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'O' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP O 14 " --> pdb=" O GLU O 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU O 90 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE O 107 " --> pdb=" O ALA O 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA O 127 " --> pdb=" O ILE O 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA O 62 " --> pdb=" O SER O 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL O 69 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU O 27 " --> pdb=" O VAL O 69 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'O' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP O 14 " --> pdb=" O GLU O 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU O 90 " --> pdb=" O ASP O 14 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP P 14 " --> pdb=" O GLU P 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU P 90 " --> pdb=" O ASP P 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE P 107 " --> pdb=" O ALA P 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA P 127 " --> pdb=" O ILE P 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA P 62 " --> pdb=" O SER P 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL P 69 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU P 27 " --> pdb=" O VAL P 69 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'P' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP P 14 " --> pdb=" O GLU P 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU P 90 " --> pdb=" O ASP P 14 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'Q' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP Q 14 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU Q 90 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE Q 107 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA Q 127 " --> pdb=" O ILE Q 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA Q 62 " --> pdb=" O SER Q 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL Q 69 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU Q 27 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'Q' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP Q 14 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU Q 90 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'R' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP R 14 " --> pdb=" O GLU R 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU R 90 " --> pdb=" O ASP R 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE R 107 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA R 127 " --> pdb=" O ILE R 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA R 62 " --> pdb=" O SER R 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL R 69 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU R 27 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'R' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP R 14 " --> pdb=" O GLU R 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU R 90 " --> pdb=" O ASP R 14 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'S' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP S 14 " --> pdb=" O GLU S 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU S 90 " --> pdb=" O ASP S 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE S 107 " --> pdb=" O ALA S 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA S 127 " --> pdb=" O ILE S 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA S 62 " --> pdb=" O SER S 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL S 69 " --> pdb=" O LEU S 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU S 27 " --> pdb=" O VAL S 69 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP S 14 " --> pdb=" O GLU S 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU S 90 " --> pdb=" O ASP S 14 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'T' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP T 14 " --> pdb=" O GLU T 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU T 90 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE T 107 " --> pdb=" O ALA T 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA T 127 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA T 62 " --> pdb=" O SER T 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL T 69 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU T 27 " --> pdb=" O VAL T 69 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'T' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP T 14 " --> pdb=" O GLU T 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU T 90 " --> pdb=" O ASP T 14 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'U' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP U 14 " --> pdb=" O GLU U 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU U 90 " --> pdb=" O ASP U 14 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL U 69 " --> pdb=" O LEU U 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU U 27 " --> pdb=" O VAL U 69 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP U 14 " --> pdb=" O GLU U 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU U 90 " --> pdb=" O ASP U 14 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'V' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP V 14 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU V 90 " --> pdb=" O ASP V 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE V 107 " --> pdb=" O ALA V 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA V 127 " --> pdb=" O ILE V 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA V 62 " --> pdb=" O SER V 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL V 69 " --> pdb=" O LEU V 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU V 27 " --> pdb=" O VAL V 69 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP V 14 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU V 90 " --> pdb=" O ASP V 14 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'W' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP W 14 " --> pdb=" O GLU W 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU W 90 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE W 107 " --> pdb=" O ALA W 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA W 127 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA W 62 " --> pdb=" O SER W 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL W 69 " --> pdb=" O LEU W 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU W 27 " --> pdb=" O VAL W 69 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'W' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP W 14 " --> pdb=" O GLU W 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU W 90 " --> pdb=" O ASP W 14 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'X' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP X 14 " --> pdb=" O GLU X 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU X 90 " --> pdb=" O ASP X 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE X 107 " --> pdb=" O ALA X 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA X 127 " --> pdb=" O ILE X 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA X 62 " --> pdb=" O SER X 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL X 69 " --> pdb=" O LEU X 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU X 27 " --> pdb=" O VAL X 69 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'X' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP X 14 " --> pdb=" O GLU X 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU X 90 " --> pdb=" O ASP X 14 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7993 1.33 - 1.45: 3061 1.45 - 1.56: 13066 1.56 - 1.67: 0 1.67 - 1.79: 96 Bond restraints: 24216 Sorted by residual: bond pdb=" CB ILE G 82 " pdb=" CG2 ILE G 82 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB ILE S 82 " pdb=" CG2 ILE S 82 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB ILE K 82 " pdb=" CG2 ILE K 82 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CB ILE W 82 " pdb=" CG2 ILE W 82 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CB ILE C 82 " pdb=" CG2 ILE C 82 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.68e+00 ... (remaining 24211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 29538 1.76 - 3.52: 2478 3.52 - 5.28: 488 5.28 - 7.04: 136 7.04 - 8.80: 72 Bond angle restraints: 32712 Sorted by residual: angle pdb=" N ILE J 95 " pdb=" CA ILE J 95 " pdb=" C ILE J 95 " ideal model delta sigma weight residual 108.95 103.71 5.24 9.80e-01 1.04e+00 2.86e+01 angle pdb=" N ILE V 95 " pdb=" CA ILE V 95 " pdb=" C ILE V 95 " ideal model delta sigma weight residual 108.95 103.71 5.24 9.80e-01 1.04e+00 2.86e+01 angle pdb=" N ILE M 95 " pdb=" CA ILE M 95 " pdb=" C ILE M 95 " ideal model delta sigma weight residual 108.95 103.73 5.22 9.80e-01 1.04e+00 2.84e+01 angle pdb=" N ILE B 95 " pdb=" CA ILE B 95 " pdb=" C ILE B 95 " ideal model delta sigma weight residual 108.95 103.73 5.22 9.80e-01 1.04e+00 2.84e+01 angle pdb=" N ILE A 95 " pdb=" CA ILE A 95 " pdb=" C ILE A 95 " ideal model delta sigma weight residual 108.95 103.74 5.21 9.80e-01 1.04e+00 2.83e+01 ... (remaining 32707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.71: 11008 8.71 - 17.42: 2192 17.42 - 26.13: 456 26.13 - 34.84: 336 34.84 - 43.55: 120 Dihedral angle restraints: 14112 sinusoidal: 5256 harmonic: 8856 Sorted by residual: dihedral pdb=" CA ILE W 95 " pdb=" C ILE W 95 " pdb=" N PRO W 96 " pdb=" CA PRO W 96 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE K 95 " pdb=" C ILE K 95 " pdb=" N PRO K 96 " pdb=" CA PRO K 96 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE I 95 " pdb=" C ILE I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 14109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2735 0.075 - 0.150: 619 0.150 - 0.225: 222 0.225 - 0.300: 48 0.300 - 0.375: 24 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CB ILE R 107 " pdb=" CA ILE R 107 " pdb=" CG1 ILE R 107 " pdb=" CG2 ILE R 107 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE F 107 " pdb=" CA ILE F 107 " pdb=" CG1 ILE F 107 " pdb=" CG2 ILE F 107 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE L 107 " pdb=" CA ILE L 107 " pdb=" CG1 ILE L 107 " pdb=" CG2 ILE L 107 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 3645 not shown) Planarity restraints: 4368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP F 72 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASP F 72 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP F 72 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 72 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP R 72 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASP R 72 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP R 72 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP R 72 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 72 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" CG ASP K 72 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP K 72 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP K 72 " 0.013 2.00e-02 2.50e+03 ... (remaining 4365 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 8590 2.85 - 3.36: 21838 3.36 - 3.87: 41197 3.87 - 4.39: 46319 4.39 - 4.90: 83080 Nonbonded interactions: 201024 Sorted by model distance: nonbonded pdb=" O GLY A 48 " pdb=" NH2 ARG F 60 " model vdw 2.334 3.120 nonbonded pdb=" O GLY N 48 " pdb=" NH2 ARG R 60 " model vdw 2.334 3.120 nonbonded pdb=" O GLY J 48 " pdb=" NH2 ARG N 60 " model vdw 2.334 3.120 nonbonded pdb=" NH2 ARG A 60 " pdb=" O GLY V 48 " model vdw 2.334 3.120 nonbonded pdb=" O GLY R 48 " pdb=" NH2 ARG V 60 " model vdw 2.334 3.120 ... (remaining 201019 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: 0.08 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' 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' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.290 Find NCS groups from input model: 0.210 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.011 0.064 24216 Z= 0.491 Angle : 1.201 8.801 32712 Z= 0.656 Chirality : 0.080 0.375 3648 Planarity : 0.006 0.049 4368 Dihedral : 11.726 43.550 8496 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % 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: -4.47 (0.12), residues: 3168 helix: -5.02 (0.04), residues: 480 sheet: -1.48 (0.16), residues: 864 loop : -3.27 (0.12), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG X 78 TYR 0.013 0.004 TYR Q 112 PHE 0.022 0.005 PHE U 98 TRP 0.020 0.004 TRP G 50 HIS 0.012 0.008 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.01074 (24216) covalent geometry : angle 1.20116 (32712) hydrogen bonds : bond 0.24231 ( 912) hydrogen bonds : angle 9.31953 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1136 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9070 (mp) cc_final: 0.8842 (mt) REVERT: B 111 ASP cc_start: 0.8524 (p0) cc_final: 0.8176 (p0) REVERT: A 28 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7648 (mmp-170) REVERT: A 91 PHE cc_start: 0.8484 (m-80) cc_final: 0.8278 (m-80) REVERT: C 14 ASP cc_start: 0.7636 (m-30) cc_final: 0.7243 (m-30) REVERT: C 18 SER cc_start: 0.8268 (p) cc_final: 0.7999 (p) REVERT: C 39 VAL cc_start: 0.8852 (p) cc_final: 0.8650 (p) REVERT: C 60 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7318 (mtm180) REVERT: D 12 LYS cc_start: 0.8785 (mttp) cc_final: 0.8486 (mtpp) REVERT: D 14 ASP cc_start: 0.7399 (m-30) cc_final: 0.7146 (m-30) REVERT: D 65 SER cc_start: 0.8538 (t) cc_final: 0.8249 (p) REVERT: D 71 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8538 (mtmm) REVERT: D 76 ASP cc_start: 0.8258 (t0) cc_final: 0.8008 (t0) REVERT: E 111 ASP cc_start: 0.8365 (p0) cc_final: 0.7965 (p0) REVERT: F 4 GLN cc_start: 0.8460 (tp40) cc_final: 0.8148 (mm-40) REVERT: F 12 LYS cc_start: 0.8443 (mttp) cc_final: 0.8100 (mmmm) REVERT: F 28 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7482 (mmp-170) REVERT: G 69 VAL cc_start: 0.9494 (m) cc_final: 0.9293 (p) REVERT: H 4 GLN cc_start: 0.8793 (tp40) cc_final: 0.8349 (mm-40) REVERT: H 14 ASP cc_start: 0.7277 (m-30) cc_final: 0.7008 (m-30) REVERT: H 15 LEU cc_start: 0.8420 (mm) cc_final: 0.7440 (mm) REVERT: H 23 THR cc_start: 0.8705 (m) cc_final: 0.8497 (p) REVERT: H 44 LEU cc_start: 0.8845 (tm) cc_final: 0.8605 (tp) REVERT: H 50 TRP cc_start: 0.8899 (m100) cc_final: 0.7495 (m100) REVERT: H 65 SER cc_start: 0.8676 (t) cc_final: 0.8374 (p) REVERT: H 92 GLN cc_start: 0.8497 (tt0) cc_final: 0.8249 (tt0) REVERT: H 117 ASN cc_start: 0.9370 (p0) cc_final: 0.9075 (p0) REVERT: I 60 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7586 (mtm110) REVERT: I 111 ASP cc_start: 0.8545 (p0) cc_final: 0.6828 (p0) REVERT: J 12 LYS cc_start: 0.8419 (mttp) cc_final: 0.7984 (mmmm) REVERT: J 28 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7683 (mmp-170) REVERT: J 52 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7689 (mt-10) REVERT: J 71 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8881 (mtpp) REVERT: J 90 GLU cc_start: 0.8020 (tp30) cc_final: 0.7686 (tp30) REVERT: J 109 SER cc_start: 0.8867 (t) cc_final: 0.8658 (m) REVERT: K 14 ASP cc_start: 0.7870 (m-30) cc_final: 0.7273 (m-30) REVERT: K 18 SER cc_start: 0.8248 (p) cc_final: 0.7980 (p) REVERT: K 92 GLN cc_start: 0.8753 (tt0) cc_final: 0.8501 (tt0) REVERT: K 111 ASP cc_start: 0.8277 (p0) cc_final: 0.7928 (p0) REVERT: K 115 SER cc_start: 0.8782 (m) cc_final: 0.8393 (p) REVERT: L 23 THR cc_start: 0.8799 (m) cc_final: 0.8463 (p) REVERT: L 65 SER cc_start: 0.8559 (t) cc_final: 0.8230 (p) REVERT: M 10 LEU cc_start: 0.9067 (mp) cc_final: 0.8842 (mt) REVERT: M 111 ASP cc_start: 0.8540 (p0) cc_final: 0.8171 (p0) REVERT: N 28 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7647 (mmp-170) REVERT: N 91 PHE cc_start: 0.8480 (m-80) cc_final: 0.8273 (m-80) REVERT: O 14 ASP cc_start: 0.7649 (m-30) cc_final: 0.7258 (m-30) REVERT: O 18 SER cc_start: 0.8270 (p) cc_final: 0.8004 (p) REVERT: O 39 VAL cc_start: 0.8847 (p) cc_final: 0.8647 (p) REVERT: O 60 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7334 (mtm180) REVERT: P 12 LYS cc_start: 0.8793 (mttp) cc_final: 0.8482 (mtpp) REVERT: P 14 ASP cc_start: 0.7393 (m-30) cc_final: 0.7139 (m-30) REVERT: P 23 THR cc_start: 0.8886 (m) cc_final: 0.8684 (p) REVERT: P 65 SER cc_start: 0.8538 (t) cc_final: 0.8245 (p) REVERT: P 76 ASP cc_start: 0.8252 (t0) cc_final: 0.8016 (t0) REVERT: Q 111 ASP cc_start: 0.8363 (p0) cc_final: 0.7967 (p0) REVERT: R 4 GLN cc_start: 0.8458 (tp40) cc_final: 0.8152 (mm-40) REVERT: R 12 LYS cc_start: 0.8444 (mttp) cc_final: 0.8100 (mmmm) REVERT: R 28 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7482 (mmp-170) REVERT: S 69 VAL cc_start: 0.9488 (m) cc_final: 0.9283 (p) REVERT: T 4 GLN cc_start: 0.8791 (tp40) cc_final: 0.8347 (mm-40) REVERT: T 14 ASP cc_start: 0.7267 (m-30) cc_final: 0.7011 (m-30) REVERT: T 15 LEU cc_start: 0.8415 (mm) cc_final: 0.7435 (mm) REVERT: T 23 THR cc_start: 0.8707 (m) cc_final: 0.8497 (p) REVERT: T 44 LEU cc_start: 0.8848 (tm) cc_final: 0.8610 (tp) REVERT: T 50 TRP cc_start: 0.8900 (m100) cc_final: 0.7503 (m100) REVERT: T 65 SER cc_start: 0.8678 (t) cc_final: 0.8376 (p) REVERT: T 92 GLN cc_start: 0.8504 (tt0) cc_final: 0.8247 (tt0) REVERT: T 117 ASN cc_start: 0.9372 (p0) cc_final: 0.9079 (p0) REVERT: U 60 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7590 (mtm110) REVERT: U 111 ASP cc_start: 0.8530 (p0) cc_final: 0.6815 (p0) REVERT: V 12 LYS cc_start: 0.8417 (mttp) cc_final: 0.7984 (mmmm) REVERT: V 28 ARG cc_start: 0.7940 (mtm180) cc_final: 0.7682 (mmp-170) REVERT: V 52 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7701 (mt-10) REVERT: V 71 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8884 (mtpp) REVERT: V 90 GLU cc_start: 0.8019 (tp30) cc_final: 0.7683 (tp30) REVERT: V 109 SER cc_start: 0.8864 (t) cc_final: 0.8655 (m) REVERT: W 14 ASP cc_start: 0.7873 (m-30) cc_final: 0.7278 (m-30) REVERT: W 18 SER cc_start: 0.8247 (p) cc_final: 0.7982 (p) REVERT: W 92 GLN cc_start: 0.8750 (tt0) cc_final: 0.8503 (tt0) REVERT: W 111 ASP cc_start: 0.8275 (p0) cc_final: 0.7943 (p0) REVERT: W 115 SER cc_start: 0.8796 (m) cc_final: 0.8409 (p) REVERT: X 23 THR cc_start: 0.8793 (m) cc_final: 0.8461 (p) REVERT: X 50 TRP cc_start: 0.8953 (m100) cc_final: 0.8207 (m100) REVERT: X 65 SER cc_start: 0.8563 (t) cc_final: 0.8235 (p) outliers start: 0 outliers final: 0 residues processed: 1136 average time/residue: 0.1563 time to fit residues: 278.8899 Evaluate side-chains 810 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 810 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 20 GLN D 92 GLN E 102 GLN E 116 HIS F 20 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN H 102 GLN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS J 81 GLN L 20 GLN L 92 GLN L 102 GLN ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 HIS ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN P 20 GLN P 92 GLN Q 102 GLN Q 116 HIS R 20 GLN ** R 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 116 HIS V 81 GLN X 20 GLN X 92 GLN X 102 GLN ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.079409 restraints weight = 47210.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082081 restraints weight = 21944.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.083817 restraints weight = 12343.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.084964 restraints weight = 7944.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085739 restraints weight = 5649.804| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24216 Z= 0.190 Angle : 0.763 7.782 32712 Z= 0.403 Chirality : 0.053 0.308 3648 Planarity : 0.005 0.035 4368 Dihedral : 6.382 28.415 3384 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.08 % Allowed : 16.50 % Favored : 79.41 % 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: -3.64 (0.12), residues: 3168 helix: -4.09 (0.10), residues: 480 sheet: -0.90 (0.16), residues: 936 loop : -2.88 (0.12), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 78 TYR 0.017 0.001 TYR V 122 PHE 0.034 0.002 PHE P 21 TRP 0.014 0.001 TRP P 50 HIS 0.008 0.001 HIS T 116 Details of bonding type rmsd covalent geometry : bond 0.00407 (24216) covalent geometry : angle 0.76328 (32712) hydrogen bonds : bond 0.05106 ( 912) hydrogen bonds : angle 6.04256 ( 2664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 950 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8654 (mttp) cc_final: 0.8399 (mtpp) REVERT: B 76 ASP cc_start: 0.8227 (t0) cc_final: 0.7839 (t0) REVERT: B 90 GLU cc_start: 0.8011 (tp30) cc_final: 0.7640 (mm-30) REVERT: B 98 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: B 123 GLU cc_start: 0.7085 (mp0) cc_final: 0.6874 (mp0) REVERT: B 126 MET cc_start: 0.8079 (mtp) cc_final: 0.7568 (mtp) REVERT: A 4 GLN cc_start: 0.8484 (tp40) cc_final: 0.7937 (mm-40) REVERT: A 12 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8068 (mmmm) REVERT: A 14 ASP cc_start: 0.7424 (m-30) cc_final: 0.7037 (m-30) REVERT: A 28 ARG cc_start: 0.8114 (mtm180) cc_final: 0.7404 (mmp-170) REVERT: A 91 PHE cc_start: 0.8585 (m-80) cc_final: 0.8290 (m-80) REVERT: C 98 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: D 15 LEU cc_start: 0.7923 (mm) cc_final: 0.7697 (mm) REVERT: D 20 GLN cc_start: 0.7240 (tt0) cc_final: 0.7015 (tt0) REVERT: D 22 GLU cc_start: 0.7044 (mp0) cc_final: 0.6683 (mp0) REVERT: D 102 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8669 (tp-100) REVERT: E 35 ASN cc_start: 0.8498 (m-40) cc_final: 0.8214 (m-40) REVERT: E 98 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: E 126 MET cc_start: 0.7690 (mtp) cc_final: 0.7488 (mtp) REVERT: F 28 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7430 (mmp-170) REVERT: F 90 GLU cc_start: 0.8459 (tp30) cc_final: 0.8180 (tp30) REVERT: G 10 LEU cc_start: 0.8825 (mp) cc_final: 0.8622 (mt) REVERT: G 69 VAL cc_start: 0.9585 (m) cc_final: 0.9339 (p) REVERT: G 98 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: G 111 ASP cc_start: 0.8279 (p0) cc_final: 0.8070 (p0) REVERT: H 23 THR cc_start: 0.8608 (m) cc_final: 0.8222 (p) REVERT: H 44 LEU cc_start: 0.8952 (tm) cc_final: 0.8635 (tp) REVERT: H 47 GLN cc_start: 0.8003 (mp10) cc_final: 0.7684 (pm20) REVERT: H 52 GLU cc_start: 0.7239 (mp0) cc_final: 0.7003 (mp0) REVERT: H 81 GLN cc_start: 0.8210 (pp30) cc_final: 0.7810 (pp30) REVERT: H 85 ASP cc_start: 0.7211 (p0) cc_final: 0.6969 (p0) REVERT: I 14 ASP cc_start: 0.7272 (m-30) cc_final: 0.6954 (m-30) REVERT: I 35 ASN cc_start: 0.8554 (m-40) cc_final: 0.8245 (m-40) REVERT: I 76 ASP cc_start: 0.8396 (t0) cc_final: 0.8015 (t0) REVERT: I 90 GLU cc_start: 0.8109 (tp30) cc_final: 0.7532 (tp30) REVERT: I 92 GLN cc_start: 0.8792 (tt0) cc_final: 0.8516 (tt0) REVERT: I 98 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: J 28 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7354 (mmp-170) REVERT: J 52 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7752 (mt-10) REVERT: J 71 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8629 (mtpp) REVERT: J 81 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: J 109 SER cc_start: 0.8932 (t) cc_final: 0.8594 (m) REVERT: J 126 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7236 (mtp) REVERT: K 98 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: K 111 ASP cc_start: 0.8467 (p0) cc_final: 0.8216 (p0) REVERT: L 20 GLN cc_start: 0.7218 (tt0) cc_final: 0.6898 (tt0) REVERT: L 23 THR cc_start: 0.8605 (m) cc_final: 0.8185 (p) REVERT: L 71 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8002 (mtmm) REVERT: L 81 GLN cc_start: 0.8393 (pp30) cc_final: 0.7886 (pp30) REVERT: L 98 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7558 (m-10) REVERT: L 134 PHE cc_start: 0.8163 (t80) cc_final: 0.7930 (t80) REVERT: M 12 LYS cc_start: 0.8658 (mttp) cc_final: 0.8392 (mtpp) REVERT: M 76 ASP cc_start: 0.8239 (t0) cc_final: 0.7857 (t0) REVERT: M 90 GLU cc_start: 0.8017 (tp30) cc_final: 0.7638 (mm-30) REVERT: M 98 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: M 123 GLU cc_start: 0.7089 (mp0) cc_final: 0.6878 (mp0) REVERT: M 126 MET cc_start: 0.8091 (mtp) cc_final: 0.7520 (mtp) REVERT: N 4 GLN cc_start: 0.8480 (tp40) cc_final: 0.7939 (mm-40) REVERT: N 12 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8069 (mmmm) REVERT: N 14 ASP cc_start: 0.7421 (m-30) cc_final: 0.7037 (m-30) REVERT: N 28 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7405 (mmp-170) REVERT: N 91 PHE cc_start: 0.8584 (m-80) cc_final: 0.8285 (m-80) REVERT: O 98 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: P 10 LEU cc_start: 0.8699 (mp) cc_final: 0.8498 (mt) REVERT: P 15 LEU cc_start: 0.7962 (mm) cc_final: 0.7729 (mm) REVERT: P 20 GLN cc_start: 0.7169 (tt0) cc_final: 0.6907 (tt0) REVERT: P 22 GLU cc_start: 0.7016 (mp0) cc_final: 0.6767 (mp0) REVERT: P 23 THR cc_start: 0.8751 (m) cc_final: 0.8400 (p) REVERT: P 102 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8664 (tp-100) REVERT: Q 35 ASN cc_start: 0.8493 (m-40) cc_final: 0.8211 (m-40) REVERT: Q 98 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: R 28 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7425 (mmp-170) REVERT: R 90 GLU cc_start: 0.8461 (tp30) cc_final: 0.8179 (tp30) REVERT: S 10 LEU cc_start: 0.8824 (mp) cc_final: 0.8619 (mt) REVERT: S 69 VAL cc_start: 0.9588 (m) cc_final: 0.9331 (p) REVERT: S 98 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: S 111 ASP cc_start: 0.8290 (p0) cc_final: 0.8077 (p0) REVERT: T 23 THR cc_start: 0.8604 (m) cc_final: 0.8219 (p) REVERT: T 44 LEU cc_start: 0.8954 (tm) cc_final: 0.8639 (tp) REVERT: T 47 GLN cc_start: 0.8003 (mp10) cc_final: 0.7683 (pm20) REVERT: T 52 GLU cc_start: 0.7231 (mp0) cc_final: 0.7000 (mp0) REVERT: T 81 GLN cc_start: 0.8175 (pp30) cc_final: 0.7787 (pp30) REVERT: T 85 ASP cc_start: 0.7168 (p0) cc_final: 0.6964 (p0) REVERT: U 14 ASP cc_start: 0.7261 (m-30) cc_final: 0.6946 (m-30) REVERT: U 35 ASN cc_start: 0.8535 (m-40) cc_final: 0.8236 (m-40) REVERT: U 76 ASP cc_start: 0.8397 (t0) cc_final: 0.8015 (t0) REVERT: U 90 GLU cc_start: 0.8104 (tp30) cc_final: 0.7530 (tp30) REVERT: U 92 GLN cc_start: 0.8791 (tt0) cc_final: 0.8512 (tt0) REVERT: U 98 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: V 28 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7355 (mmp-170) REVERT: V 52 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7765 (mt-10) REVERT: V 71 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8635 (mtpp) REVERT: V 81 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8066 (pp30) REVERT: V 109 SER cc_start: 0.8928 (t) cc_final: 0.8593 (m) REVERT: V 126 MET cc_start: 0.7696 (mtp) cc_final: 0.7258 (mtp) REVERT: W 98 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7949 (m-10) REVERT: W 111 ASP cc_start: 0.8461 (p0) cc_final: 0.8220 (p0) REVERT: X 20 GLN cc_start: 0.7214 (tt0) cc_final: 0.6903 (tt0) REVERT: X 23 THR cc_start: 0.8617 (m) cc_final: 0.8188 (p) REVERT: X 47 GLN cc_start: 0.7967 (mp10) cc_final: 0.7491 (mp10) REVERT: X 50 TRP cc_start: 0.8919 (m100) cc_final: 0.8522 (m100) REVERT: X 71 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7992 (mtmm) REVERT: X 81 GLN cc_start: 0.8383 (pp30) cc_final: 0.7880 (pp30) REVERT: X 98 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7541 (m-10) outliers start: 99 outliers final: 40 residues processed: 998 average time/residue: 0.1602 time to fit residues: 249.2487 Evaluate side-chains 866 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 807 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 81 GLN Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 233 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 116 HIS D 92 GLN D 102 GLN F 20 GLN G 116 HIS H 92 GLN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN K 116 HIS ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN O 116 HIS P 92 GLN P 102 GLN R 20 GLN S 116 HIS T 92 GLN T 102 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN W 116 HIS ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.070058 restraints weight = 49787.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.072554 restraints weight = 23645.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.074226 restraints weight = 13560.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.075332 restraints weight = 8836.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.076063 restraints weight = 6361.279| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 24216 Z= 0.407 Angle : 0.861 8.539 32712 Z= 0.459 Chirality : 0.056 0.371 3648 Planarity : 0.005 0.035 4368 Dihedral : 6.635 29.338 3384 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 5.45 % Allowed : 20.30 % Favored : 74.26 % 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: -3.19 (0.13), residues: 3168 helix: -3.01 (0.16), residues: 480 sheet: -1.17 (0.14), residues: 1200 loop : -2.58 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG W 51 TYR 0.015 0.003 TYR F 122 PHE 0.032 0.003 PHE Q 91 TRP 0.015 0.003 TRP T 50 HIS 0.008 0.003 HIS X 116 Details of bonding type rmsd covalent geometry : bond 0.00916 (24216) covalent geometry : angle 0.86144 (32712) hydrogen bonds : bond 0.05467 ( 912) hydrogen bonds : angle 5.86934 ( 2664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 827 time to evaluate : 0.784 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: B 12 LYS cc_start: 0.8948 (mttp) cc_final: 0.8532 (mtpp) REVERT: B 37 GLU cc_start: 0.7856 (tp30) cc_final: 0.7389 (mm-30) REVERT: B 47 GLN cc_start: 0.8555 (pm20) cc_final: 0.8273 (pm20) REVERT: B 76 ASP cc_start: 0.8369 (t0) cc_final: 0.7923 (t0) REVERT: B 78 ARG cc_start: 0.9113 (tpt90) cc_final: 0.8505 (tpt-90) REVERT: B 98 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: A 4 GLN cc_start: 0.8566 (tp40) cc_final: 0.8243 (mm-40) REVERT: A 14 ASP cc_start: 0.7395 (m-30) cc_final: 0.7081 (m-30) REVERT: A 28 ARG cc_start: 0.8624 (mtm180) cc_final: 0.7574 (mmp-170) REVERT: A 117 ASN cc_start: 0.9146 (p0) cc_final: 0.8804 (p0) REVERT: C 77 GLU cc_start: 0.9239 (tp30) cc_final: 0.9012 (tp30) REVERT: C 98 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: C 110 ILE cc_start: 0.9261 (tp) cc_final: 0.8963 (tp) REVERT: C 134 PHE cc_start: 0.8721 (t80) cc_final: 0.8179 (t80) REVERT: D 47 GLN cc_start: 0.8284 (mp10) cc_final: 0.8079 (mp10) REVERT: D 50 TRP cc_start: 0.8805 (m100) cc_final: 0.8450 (m100) REVERT: D 60 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7284 (mtm110) REVERT: D 76 ASP cc_start: 0.8021 (t0) cc_final: 0.7798 (t0) REVERT: D 98 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: E 37 GLU cc_start: 0.8037 (tp30) cc_final: 0.7678 (mm-30) REVERT: E 76 ASP cc_start: 0.8402 (t0) cc_final: 0.7699 (t0) REVERT: E 98 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: F 4 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8403 (mm-40) REVERT: F 28 ARG cc_start: 0.8622 (mtm180) cc_final: 0.7456 (mmt180) REVERT: F 98 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: F 117 ASN cc_start: 0.9224 (p0) cc_final: 0.9001 (p0) REVERT: G 98 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: G 111 ASP cc_start: 0.8590 (p0) cc_final: 0.8386 (p0) REVERT: G 134 PHE cc_start: 0.8462 (t80) cc_final: 0.8251 (t80) REVERT: H 22 GLU cc_start: 0.7070 (mp0) cc_final: 0.6847 (mp0) REVERT: H 23 THR cc_start: 0.8785 (m) cc_final: 0.8519 (p) REVERT: H 44 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8970 (tt) REVERT: H 47 GLN cc_start: 0.8223 (mp10) cc_final: 0.8020 (mp10) REVERT: H 50 TRP cc_start: 0.8288 (m100) cc_final: 0.7550 (m100) REVERT: H 52 GLU cc_start: 0.7142 (mp0) cc_final: 0.6928 (mp0) REVERT: H 98 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7679 (m-10) REVERT: I 76 ASP cc_start: 0.8679 (t0) cc_final: 0.8113 (t0) REVERT: I 78 ARG cc_start: 0.8956 (tpt90) cc_final: 0.8385 (tpt-90) REVERT: I 98 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: J 28 ARG cc_start: 0.8591 (mtm180) cc_final: 0.7453 (mmp-170) REVERT: J 52 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7930 (mt-10) REVERT: J 71 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8880 (mtpp) REVERT: J 76 ASP cc_start: 0.8135 (t0) cc_final: 0.7915 (t0) REVERT: J 78 ARG cc_start: 0.9028 (tpt-90) cc_final: 0.8777 (tpt170) REVERT: J 117 ASN cc_start: 0.9153 (p0) cc_final: 0.8816 (p0) REVERT: K 98 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: L 8 ASP cc_start: 0.7673 (m-30) cc_final: 0.7440 (m-30) REVERT: L 22 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6941 (mm-30) REVERT: L 23 THR cc_start: 0.8862 (m) cc_final: 0.8575 (p) REVERT: L 70 PHE cc_start: 0.8985 (t80) cc_final: 0.8462 (t80) REVERT: L 98 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7728 (m-10) REVERT: L 134 PHE cc_start: 0.8290 (t80) cc_final: 0.8069 (t80) REVERT: M 12 LYS cc_start: 0.8952 (mttp) cc_final: 0.8523 (mtpp) REVERT: M 37 GLU cc_start: 0.7847 (tp30) cc_final: 0.7375 (mm-30) REVERT: M 47 GLN cc_start: 0.8569 (pm20) cc_final: 0.8285 (pm20) REVERT: M 76 ASP cc_start: 0.8378 (t0) cc_final: 0.7943 (t0) REVERT: M 78 ARG cc_start: 0.9113 (tpt90) cc_final: 0.8532 (tpt-90) REVERT: M 98 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: N 4 GLN cc_start: 0.8564 (tp40) cc_final: 0.8249 (mm-40) REVERT: N 14 ASP cc_start: 0.7394 (m-30) cc_final: 0.7083 (m-30) REVERT: N 28 ARG cc_start: 0.8626 (mtm180) cc_final: 0.7575 (mmp-170) REVERT: N 117 ASN cc_start: 0.9142 (p0) cc_final: 0.8805 (p0) REVERT: O 20 GLN cc_start: 0.7898 (tp40) cc_final: 0.7570 (tp-100) REVERT: O 98 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: O 110 ILE cc_start: 0.9254 (tp) cc_final: 0.8958 (tp) REVERT: O 134 PHE cc_start: 0.8714 (t80) cc_final: 0.8179 (t80) REVERT: P 10 LEU cc_start: 0.8864 (mp) cc_final: 0.8531 (mt) REVERT: P 22 GLU cc_start: 0.7102 (mp0) cc_final: 0.6880 (mp0) REVERT: P 23 THR cc_start: 0.8887 (m) cc_final: 0.8531 (p) REVERT: P 50 TRP cc_start: 0.8805 (m100) cc_final: 0.8455 (m100) REVERT: P 98 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: Q 37 GLU cc_start: 0.8034 (tp30) cc_final: 0.7689 (mm-30) REVERT: Q 76 ASP cc_start: 0.8370 (t0) cc_final: 0.7631 (t0) REVERT: Q 98 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: R 4 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8398 (mm-40) REVERT: R 28 ARG cc_start: 0.8619 (mtm180) cc_final: 0.7460 (mmt180) REVERT: R 98 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: R 117 ASN cc_start: 0.9222 (p0) cc_final: 0.9000 (p0) REVERT: S 98 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: S 111 ASP cc_start: 0.8596 (p0) cc_final: 0.8385 (p0) REVERT: S 134 PHE cc_start: 0.8453 (t80) cc_final: 0.8248 (t80) REVERT: T 22 GLU cc_start: 0.7081 (mp0) cc_final: 0.6845 (mp0) REVERT: T 23 THR cc_start: 0.8779 (m) cc_final: 0.8513 (p) REVERT: T 44 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8971 (tt) REVERT: T 47 GLN cc_start: 0.8227 (mp10) cc_final: 0.8022 (mp10) REVERT: T 50 TRP cc_start: 0.8295 (m100) cc_final: 0.7559 (m100) REVERT: T 52 GLU cc_start: 0.7151 (mp0) cc_final: 0.6942 (mp0) REVERT: T 76 ASP cc_start: 0.7860 (t0) cc_final: 0.7591 (t0) REVERT: T 98 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: U 76 ASP cc_start: 0.8672 (t0) cc_final: 0.8098 (t0) REVERT: U 78 ARG cc_start: 0.8960 (tpt90) cc_final: 0.8395 (tpt-90) REVERT: U 98 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: V 28 ARG cc_start: 0.8590 (mtm180) cc_final: 0.7456 (mmp-170) REVERT: V 52 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7955 (mt-10) REVERT: V 71 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8884 (mtpp) REVERT: V 76 ASP cc_start: 0.8137 (t0) cc_final: 0.7922 (t0) REVERT: V 78 ARG cc_start: 0.9026 (tpt-90) cc_final: 0.8779 (tpt170) REVERT: V 117 ASN cc_start: 0.9148 (p0) cc_final: 0.8816 (p0) REVERT: W 98 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: W 134 PHE cc_start: 0.8404 (t80) cc_final: 0.8142 (t80) REVERT: X 8 ASP cc_start: 0.7713 (m-30) cc_final: 0.7454 (m-30) REVERT: X 22 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6945 (mm-30) REVERT: X 23 THR cc_start: 0.8872 (m) cc_final: 0.8580 (p) REVERT: X 50 TRP cc_start: 0.8925 (m100) cc_final: 0.8493 (m100) REVERT: X 70 PHE cc_start: 0.8984 (t80) cc_final: 0.8458 (t80) REVERT: X 98 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7328 (m-10) outliers start: 132 outliers final: 67 residues processed: 878 average time/residue: 0.1563 time to fit residues: 216.8226 Evaluate side-chains 832 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 743 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 126 MET Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 123 GLU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 75 THR Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN E 102 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 GLN Q 102 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 102 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.077399 restraints weight = 47431.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.079987 restraints weight = 22015.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.081650 restraints weight = 12431.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082724 restraints weight = 7969.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083462 restraints weight = 5701.323| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24216 Z= 0.161 Angle : 0.718 8.145 32712 Z= 0.369 Chirality : 0.051 0.277 3648 Planarity : 0.004 0.023 4368 Dihedral : 5.976 28.966 3384 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.90 % Allowed : 20.50 % Favored : 73.60 % 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: -2.95 (0.13), residues: 3168 helix: -2.19 (0.20), residues: 480 sheet: -1.14 (0.14), residues: 1224 loop : -2.56 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 60 TYR 0.014 0.001 TYR N 122 PHE 0.016 0.002 PHE H 21 TRP 0.008 0.001 TRP H 50 HIS 0.006 0.002 HIS T 116 Details of bonding type rmsd covalent geometry : bond 0.00357 (24216) covalent geometry : angle 0.71807 (32712) hydrogen bonds : bond 0.04112 ( 912) hydrogen bonds : angle 5.19547 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 879 time to evaluate : 0.791 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: B 35 ASN cc_start: 0.8527 (m-40) cc_final: 0.8076 (m110) REVERT: B 47 GLN cc_start: 0.8503 (pm20) cc_final: 0.8263 (pm20) REVERT: B 76 ASP cc_start: 0.8148 (t0) cc_final: 0.7720 (t0) REVERT: B 78 ARG cc_start: 0.8984 (tpt90) cc_final: 0.8616 (tpt-90) REVERT: B 98 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 132 LEU cc_start: 0.8484 (mm) cc_final: 0.8239 (mt) REVERT: A 4 GLN cc_start: 0.8334 (tp40) cc_final: 0.7913 (mm-40) REVERT: A 28 ARG cc_start: 0.8461 (mtm180) cc_final: 0.7370 (mmp-170) REVERT: A 90 GLU cc_start: 0.7964 (tp30) cc_final: 0.7452 (mm-30) REVERT: A 98 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: A 117 ASN cc_start: 0.9125 (p0) cc_final: 0.8738 (p0) REVERT: C 98 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8142 (m-10) REVERT: C 134 PHE cc_start: 0.8492 (t80) cc_final: 0.8081 (t80) REVERT: D 98 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: E 76 ASP cc_start: 0.8286 (t0) cc_final: 0.7921 (t0) REVERT: E 98 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: E 134 PHE cc_start: 0.8585 (t80) cc_final: 0.8108 (t80) REVERT: F 4 GLN cc_start: 0.8596 (mm-40) cc_final: 0.7999 (mm-40) REVERT: F 28 ARG cc_start: 0.8446 (mtm180) cc_final: 0.7404 (mmp-170) REVERT: F 98 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: G 10 LEU cc_start: 0.9145 (mp) cc_final: 0.8924 (mp) REVERT: G 98 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: H 23 THR cc_start: 0.8412 (m) cc_final: 0.8010 (p) REVERT: H 50 TRP cc_start: 0.8336 (m100) cc_final: 0.7567 (m100) REVERT: H 52 GLU cc_start: 0.7180 (mp0) cc_final: 0.6968 (mp0) REVERT: H 76 ASP cc_start: 0.7822 (t0) cc_final: 0.7555 (t0) REVERT: H 98 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: I 14 ASP cc_start: 0.7190 (m-30) cc_final: 0.6836 (m-30) REVERT: I 35 ASN cc_start: 0.8559 (m-40) cc_final: 0.8315 (m-40) REVERT: I 76 ASP cc_start: 0.8452 (t0) cc_final: 0.8019 (t0) REVERT: I 98 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: J 4 GLN cc_start: 0.8658 (mm-40) cc_final: 0.7996 (mm-40) REVERT: J 28 ARG cc_start: 0.8344 (mtm180) cc_final: 0.7434 (mmp-170) REVERT: J 71 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8795 (mtpp) REVERT: J 100 ILE cc_start: 0.8888 (mm) cc_final: 0.8573 (mm) REVERT: J 117 ASN cc_start: 0.9169 (p0) cc_final: 0.8784 (p0) REVERT: J 126 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7076 (mtt) REVERT: K 60 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7606 (mtm180) REVERT: K 77 GLU cc_start: 0.9087 (tp30) cc_final: 0.8859 (tp30) REVERT: K 98 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8127 (m-10) REVERT: L 23 THR cc_start: 0.8557 (m) cc_final: 0.7998 (p) REVERT: L 98 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: M 35 ASN cc_start: 0.8524 (m-40) cc_final: 0.8052 (m110) REVERT: M 47 GLN cc_start: 0.8513 (pm20) cc_final: 0.8273 (pm20) REVERT: M 76 ASP cc_start: 0.8153 (t0) cc_final: 0.7722 (t0) REVERT: M 78 ARG cc_start: 0.8980 (tpt90) cc_final: 0.8614 (tpt-90) REVERT: M 98 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: M 132 LEU cc_start: 0.8481 (mm) cc_final: 0.8235 (mt) REVERT: N 4 GLN cc_start: 0.8331 (tp40) cc_final: 0.7916 (mm-40) REVERT: N 28 ARG cc_start: 0.8458 (mtm180) cc_final: 0.7362 (mmp-170) REVERT: N 90 GLU cc_start: 0.7959 (tp30) cc_final: 0.7449 (mm-30) REVERT: N 98 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: N 117 ASN cc_start: 0.9123 (p0) cc_final: 0.8732 (p0) REVERT: O 98 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8148 (m-10) REVERT: O 134 PHE cc_start: 0.8489 (t80) cc_final: 0.8079 (t80) REVERT: P 21 PHE cc_start: 0.8337 (m-80) cc_final: 0.8094 (m-10) REVERT: P 76 ASP cc_start: 0.7729 (t0) cc_final: 0.7491 (t0) REVERT: Q 76 ASP cc_start: 0.8282 (t0) cc_final: 0.7880 (t0) REVERT: Q 98 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: Q 126 MET cc_start: 0.7488 (mtp) cc_final: 0.7191 (mtp) REVERT: Q 134 PHE cc_start: 0.8597 (t80) cc_final: 0.8108 (t80) REVERT: R 4 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8000 (mm-40) REVERT: R 28 ARG cc_start: 0.8457 (mtm180) cc_final: 0.7409 (mmp-170) REVERT: R 98 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: S 10 LEU cc_start: 0.9141 (mp) cc_final: 0.8923 (mp) REVERT: S 98 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: T 23 THR cc_start: 0.8407 (m) cc_final: 0.8013 (p) REVERT: T 50 TRP cc_start: 0.8341 (m100) cc_final: 0.7574 (m100) REVERT: T 52 GLU cc_start: 0.7178 (mp0) cc_final: 0.6952 (mp0) REVERT: T 98 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: U 14 ASP cc_start: 0.7200 (m-30) cc_final: 0.6836 (m-30) REVERT: U 35 ASN cc_start: 0.8546 (m-40) cc_final: 0.8301 (m-40) REVERT: U 76 ASP cc_start: 0.8454 (t0) cc_final: 0.8015 (t0) REVERT: U 98 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: V 4 GLN cc_start: 0.8657 (mm-40) cc_final: 0.7998 (mm-40) REVERT: V 28 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7427 (mmp-170) REVERT: V 71 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8800 (mtpp) REVERT: V 100 ILE cc_start: 0.8867 (mm) cc_final: 0.8543 (mm) REVERT: V 117 ASN cc_start: 0.9167 (p0) cc_final: 0.8783 (p0) REVERT: W 60 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7608 (mtm180) REVERT: W 77 GLU cc_start: 0.9081 (tp30) cc_final: 0.8856 (tp30) REVERT: W 98 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8036 (m-10) REVERT: W 134 PHE cc_start: 0.8287 (t80) cc_final: 0.8083 (t80) REVERT: X 23 THR cc_start: 0.8560 (m) cc_final: 0.8006 (p) REVERT: X 59 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8684 (p) REVERT: X 98 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7882 (m-10) outliers start: 143 outliers final: 59 residues processed: 946 average time/residue: 0.1486 time to fit residues: 224.2773 Evaluate side-chains 832 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 750 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 123 GLU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 92 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 HIS F 117 ASN G 92 GLN H 92 GLN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN K 92 GLN L 20 GLN ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN P 92 GLN R 116 HIS R 117 ASN S 92 GLN T 92 GLN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 102 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN X 20 GLN ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.082170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.070719 restraints weight = 49059.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.073207 restraints weight = 23054.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.074847 restraints weight = 13162.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.075932 restraints weight = 8562.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.076667 restraints weight = 6149.749| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 24216 Z= 0.349 Angle : 0.845 9.626 32712 Z= 0.436 Chirality : 0.056 0.369 3648 Planarity : 0.005 0.043 4368 Dihedral : 6.292 28.631 3384 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.90 % Allowed : 22.15 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.13), residues: 3168 helix: -1.76 (0.21), residues: 480 sheet: -1.44 (0.13), residues: 1344 loop : -2.39 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.015 0.002 TYR R 122 PHE 0.018 0.002 PHE U 134 TRP 0.010 0.002 TRP A 50 HIS 0.008 0.003 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00792 (24216) covalent geometry : angle 0.84492 (32712) hydrogen bonds : bond 0.04697 ( 912) hydrogen bonds : angle 5.41861 ( 2664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 756 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 GLN cc_start: 0.8575 (pm20) cc_final: 0.8317 (pm20) REVERT: B 76 ASP cc_start: 0.8426 (t0) cc_final: 0.7897 (t0) REVERT: B 98 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: A 4 GLN cc_start: 0.8522 (tp40) cc_final: 0.8115 (mm-40) REVERT: A 12 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8426 (mtpp) REVERT: A 28 ARG cc_start: 0.8654 (mtm180) cc_final: 0.7313 (mmp-170) REVERT: A 76 ASP cc_start: 0.8022 (t0) cc_final: 0.7630 (t0) REVERT: A 98 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: A 117 ASN cc_start: 0.9164 (p0) cc_final: 0.8915 (p0) REVERT: C 98 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: C 110 ILE cc_start: 0.9147 (tp) cc_final: 0.8943 (tp) REVERT: C 134 PHE cc_start: 0.8778 (t80) cc_final: 0.8271 (t80) REVERT: D 8 ASP cc_start: 0.7751 (m-30) cc_final: 0.7441 (m-30) REVERT: D 22 GLU cc_start: 0.7112 (mp0) cc_final: 0.6816 (mp0) REVERT: D 76 ASP cc_start: 0.8016 (t0) cc_final: 0.7765 (t0) REVERT: D 98 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: D 110 ILE cc_start: 0.9018 (tp) cc_final: 0.8749 (tp) REVERT: E 76 ASP cc_start: 0.8467 (t0) cc_final: 0.7888 (t0) REVERT: E 90 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: E 98 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: E 134 PHE cc_start: 0.8590 (t80) cc_final: 0.8163 (t80) REVERT: F 28 ARG cc_start: 0.8736 (mtm180) cc_final: 0.7363 (mmp-170) REVERT: F 98 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: G 37 GLU cc_start: 0.7926 (tp30) cc_final: 0.7683 (tp30) REVERT: G 98 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: H 23 THR cc_start: 0.8725 (m) cc_final: 0.8414 (p) REVERT: H 45 GLU cc_start: 0.7420 (pm20) cc_final: 0.7173 (pp20) REVERT: H 50 TRP cc_start: 0.8497 (m100) cc_final: 0.7245 (m100) REVERT: H 52 GLU cc_start: 0.7163 (mp0) cc_final: 0.6828 (mp0) REVERT: H 76 ASP cc_start: 0.8119 (t0) cc_final: 0.7876 (t0) REVERT: H 87 GLU cc_start: 0.8456 (pt0) cc_final: 0.8228 (pt0) REVERT: H 98 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7515 (m-10) REVERT: I 76 ASP cc_start: 0.8719 (t0) cc_final: 0.8119 (t0) REVERT: I 98 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: J 4 GLN cc_start: 0.8720 (mm-40) cc_final: 0.7952 (mm-40) REVERT: J 28 ARG cc_start: 0.8728 (mtm180) cc_final: 0.7379 (mmp-170) REVERT: J 71 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8953 (mtpp) REVERT: J 98 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: J 117 ASN cc_start: 0.9164 (p0) cc_final: 0.8915 (p0) REVERT: K 37 GLU cc_start: 0.7865 (tp30) cc_final: 0.7660 (tp30) REVERT: K 60 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7716 (mtm180) REVERT: K 98 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: L 8 ASP cc_start: 0.7904 (m-30) cc_final: 0.7603 (m-30) REVERT: L 23 THR cc_start: 0.8411 (m) cc_final: 0.7941 (p) REVERT: L 76 ASP cc_start: 0.8106 (t0) cc_final: 0.7839 (t0) REVERT: L 92 GLN cc_start: 0.8626 (tt0) cc_final: 0.8339 (tt0) REVERT: L 98 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: L 102 GLN cc_start: 0.8692 (tp40) cc_final: 0.8432 (tp-100) REVERT: M 47 GLN cc_start: 0.8596 (pm20) cc_final: 0.8336 (pm20) REVERT: M 76 ASP cc_start: 0.8436 (t0) cc_final: 0.7903 (t0) REVERT: M 98 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: N 4 GLN cc_start: 0.8521 (tp40) cc_final: 0.8116 (mm-40) REVERT: N 12 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8418 (mtpp) REVERT: N 28 ARG cc_start: 0.8654 (mtm180) cc_final: 0.7309 (mmp-170) REVERT: N 98 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: N 117 ASN cc_start: 0.9162 (p0) cc_final: 0.8907 (p0) REVERT: O 98 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: O 110 ILE cc_start: 0.9146 (tp) cc_final: 0.8938 (tp) REVERT: O 134 PHE cc_start: 0.8781 (t80) cc_final: 0.8274 (t80) REVERT: P 8 ASP cc_start: 0.7737 (m-30) cc_final: 0.7411 (m-30) REVERT: P 14 ASP cc_start: 0.7449 (m-30) cc_final: 0.7181 (m-30) REVERT: P 22 GLU cc_start: 0.7177 (mp0) cc_final: 0.6914 (mp0) REVERT: P 76 ASP cc_start: 0.8139 (t0) cc_final: 0.7877 (t0) REVERT: P 92 GLN cc_start: 0.8677 (tt0) cc_final: 0.8465 (tt0) REVERT: P 98 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: P 102 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8657 (tp-100) REVERT: P 110 ILE cc_start: 0.9023 (tp) cc_final: 0.8751 (tp) REVERT: Q 76 ASP cc_start: 0.8471 (t0) cc_final: 0.7885 (t0) REVERT: Q 90 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: Q 98 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: Q 134 PHE cc_start: 0.8605 (t80) cc_final: 0.8182 (t80) REVERT: R 28 ARG cc_start: 0.8736 (mtm180) cc_final: 0.7368 (mmp-170) REVERT: R 98 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: S 37 GLU cc_start: 0.7915 (tp30) cc_final: 0.7684 (tp30) REVERT: S 98 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: T 22 GLU cc_start: 0.7214 (mp0) cc_final: 0.6887 (mp0) REVERT: T 23 THR cc_start: 0.8731 (m) cc_final: 0.8409 (p) REVERT: T 45 GLU cc_start: 0.7412 (pm20) cc_final: 0.7179 (pp20) REVERT: T 50 TRP cc_start: 0.8458 (m100) cc_final: 0.7253 (m100) REVERT: T 52 GLU cc_start: 0.7169 (mp0) cc_final: 0.6861 (mp0) REVERT: T 92 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8478 (mt0) REVERT: T 98 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7511 (m-10) REVERT: U 76 ASP cc_start: 0.8716 (t0) cc_final: 0.8104 (t0) REVERT: U 98 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: V 4 GLN cc_start: 0.8724 (mm-40) cc_final: 0.7949 (mm-40) REVERT: V 28 ARG cc_start: 0.8739 (mtm180) cc_final: 0.7396 (mmp-170) REVERT: V 71 LYS cc_start: 0.9215 (mtpt) cc_final: 0.8957 (mtpp) REVERT: V 98 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: V 117 ASN cc_start: 0.9162 (p0) cc_final: 0.8912 (p0) REVERT: W 37 GLU cc_start: 0.7873 (tp30) cc_final: 0.7669 (tp30) REVERT: W 60 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7729 (mtm180) REVERT: W 77 GLU cc_start: 0.9191 (tp30) cc_final: 0.8984 (tp30) REVERT: W 98 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: W 134 PHE cc_start: 0.8537 (t80) cc_final: 0.8242 (t80) REVERT: X 8 ASP cc_start: 0.7872 (m-30) cc_final: 0.7540 (m-30) REVERT: X 23 THR cc_start: 0.8462 (m) cc_final: 0.7990 (p) REVERT: X 76 ASP cc_start: 0.8105 (t0) cc_final: 0.7840 (t0) REVERT: X 92 GLN cc_start: 0.8718 (tt0) cc_final: 0.8269 (tt0) REVERT: X 98 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7397 (m-10) outliers start: 143 outliers final: 79 residues processed: 827 average time/residue: 0.1478 time to fit residues: 197.0116 Evaluate side-chains 803 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 695 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 92 GLN Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 123 GLU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 75 THR Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 24 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 251 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN A 92 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 102 GLN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN J 102 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN S 102 GLN T 92 GLN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.075254 restraints weight = 47764.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.077842 restraints weight = 22233.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.079500 restraints weight = 12523.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.080597 restraints weight = 8064.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.081325 restraints weight = 5753.929| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24216 Z= 0.191 Angle : 0.774 9.944 32712 Z= 0.387 Chirality : 0.053 0.321 3648 Planarity : 0.004 0.031 4368 Dihedral : 5.942 27.846 3384 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.40 % Allowed : 23.60 % Favored : 71.00 % 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: -2.86 (0.13), residues: 3168 helix: -1.62 (0.21), residues: 480 sheet: -1.20 (0.13), residues: 1224 loop : -2.59 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 60 TYR 0.009 0.001 TYR B 112 PHE 0.015 0.002 PHE H 21 TRP 0.009 0.001 TRP X 50 HIS 0.006 0.002 HIS T 116 Details of bonding type rmsd covalent geometry : bond 0.00433 (24216) covalent geometry : angle 0.77354 (32712) hydrogen bonds : bond 0.03990 ( 912) hydrogen bonds : angle 5.10025 ( 2664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 781 time to evaluate : 0.870 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: B 33 SER cc_start: 0.9229 (t) cc_final: 0.8655 (p) REVERT: B 47 GLN cc_start: 0.8569 (pm20) cc_final: 0.8314 (pm20) REVERT: B 76 ASP cc_start: 0.8281 (t0) cc_final: 0.8045 (t0) REVERT: B 98 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: A 4 GLN cc_start: 0.8469 (tp40) cc_final: 0.8083 (mm-40) REVERT: A 12 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8458 (mtpp) REVERT: A 28 ARG cc_start: 0.8494 (mtm180) cc_final: 0.7018 (mmp-170) REVERT: A 76 ASP cc_start: 0.7952 (t0) cc_final: 0.7580 (t0) REVERT: A 98 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: A 117 ASN cc_start: 0.9204 (p0) cc_final: 0.8947 (p0) REVERT: C 98 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: C 134 PHE cc_start: 0.8728 (t80) cc_final: 0.8180 (t80) REVERT: D 8 ASP cc_start: 0.7701 (m-30) cc_final: 0.7331 (m-30) REVERT: D 22 GLU cc_start: 0.6904 (mp0) cc_final: 0.6542 (mp0) REVERT: D 45 GLU cc_start: 0.7430 (pm20) cc_final: 0.7125 (pp20) REVERT: D 76 ASP cc_start: 0.7940 (t0) cc_final: 0.7648 (t0) REVERT: D 98 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: D 110 ILE cc_start: 0.9047 (tp) cc_final: 0.8832 (tp) REVERT: E 76 ASP cc_start: 0.8557 (t0) cc_final: 0.8024 (t0) REVERT: E 90 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: E 98 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: E 134 PHE cc_start: 0.8515 (t80) cc_final: 0.8060 (t80) REVERT: F 4 GLN cc_start: 0.8610 (mm-40) cc_final: 0.7824 (mm-40) REVERT: F 28 ARG cc_start: 0.8626 (mtm180) cc_final: 0.7321 (mmp-170) REVERT: F 98 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: G 76 ASP cc_start: 0.8244 (t0) cc_final: 0.8043 (t0) REVERT: G 98 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8520 (m-10) REVERT: H 23 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8307 (p) REVERT: H 52 GLU cc_start: 0.7128 (mp0) cc_final: 0.6836 (mp0) REVERT: H 76 ASP cc_start: 0.8019 (t0) cc_final: 0.7800 (t0) REVERT: H 98 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: I 35 ASN cc_start: 0.8624 (m-40) cc_final: 0.8333 (m-40) REVERT: I 76 ASP cc_start: 0.8547 (t0) cc_final: 0.7957 (t0) REVERT: I 98 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7231 (m-10) REVERT: J 4 GLN cc_start: 0.8600 (mm-40) cc_final: 0.7956 (mm-40) REVERT: J 28 ARG cc_start: 0.8542 (mtm180) cc_final: 0.7176 (mmt180) REVERT: J 71 LYS cc_start: 0.9203 (mtpt) cc_final: 0.8896 (mtpp) REVERT: J 98 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: J 117 ASN cc_start: 0.9205 (p0) cc_final: 0.8929 (p0) REVERT: K 60 ARG cc_start: 0.8192 (mtm110) cc_final: 0.7914 (ptp-170) REVERT: K 98 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: L 76 ASP cc_start: 0.8076 (t0) cc_final: 0.7871 (t0) REVERT: L 102 GLN cc_start: 0.8615 (tp40) cc_final: 0.8347 (tp-100) REVERT: L 123 GLU cc_start: 0.7887 (mp0) cc_final: 0.7638 (mp0) REVERT: M 33 SER cc_start: 0.9234 (t) cc_final: 0.8688 (p) REVERT: M 47 GLN cc_start: 0.8585 (pm20) cc_final: 0.8326 (pm20) REVERT: M 76 ASP cc_start: 0.8309 (t0) cc_final: 0.8071 (t0) REVERT: M 92 GLN cc_start: 0.8960 (tt0) cc_final: 0.8303 (tt0) REVERT: M 98 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: N 4 GLN cc_start: 0.8464 (tp40) cc_final: 0.8082 (mm-40) REVERT: N 12 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8460 (mtpp) REVERT: N 28 ARG cc_start: 0.8492 (mtm180) cc_final: 0.7010 (mmp-170) REVERT: N 98 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: N 117 ASN cc_start: 0.9208 (p0) cc_final: 0.8957 (p0) REVERT: O 98 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8080 (m-10) REVERT: O 134 PHE cc_start: 0.8725 (t80) cc_final: 0.8179 (t80) REVERT: P 8 ASP cc_start: 0.7717 (m-30) cc_final: 0.7355 (m-30) REVERT: P 14 ASP cc_start: 0.7487 (m-30) cc_final: 0.7207 (m-30) REVERT: P 45 GLU cc_start: 0.7414 (pm20) cc_final: 0.7058 (pp20) REVERT: P 98 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: P 110 ILE cc_start: 0.9050 (tp) cc_final: 0.8827 (tp) REVERT: Q 76 ASP cc_start: 0.8586 (t0) cc_final: 0.8079 (t0) REVERT: Q 90 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: Q 98 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: Q 134 PHE cc_start: 0.8526 (t80) cc_final: 0.8064 (t80) REVERT: R 4 GLN cc_start: 0.8600 (mm-40) cc_final: 0.7815 (mm-40) REVERT: R 28 ARG cc_start: 0.8633 (mtm180) cc_final: 0.7324 (mmp-170) REVERT: R 98 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: S 98 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8421 (m-10) REVERT: T 23 THR cc_start: 0.8557 (m) cc_final: 0.8130 (p) REVERT: T 45 GLU cc_start: 0.7250 (pm20) cc_final: 0.7012 (pp20) REVERT: T 46 SER cc_start: 0.8531 (m) cc_final: 0.7818 (m) REVERT: T 50 TRP cc_start: 0.8438 (m100) cc_final: 0.6879 (m100) REVERT: T 52 GLU cc_start: 0.7164 (mp0) cc_final: 0.6468 (mp0) REVERT: T 76 ASP cc_start: 0.7771 (t0) cc_final: 0.7447 (t0) REVERT: T 98 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: U 35 ASN cc_start: 0.8613 (m-40) cc_final: 0.8328 (m-40) REVERT: U 76 ASP cc_start: 0.8558 (t0) cc_final: 0.7955 (t0) REVERT: U 98 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: V 4 GLN cc_start: 0.8600 (mm-40) cc_final: 0.7954 (mm-40) REVERT: V 28 ARG cc_start: 0.8522 (mtm180) cc_final: 0.7144 (mmt180) REVERT: V 71 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8901 (mtpp) REVERT: V 98 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: V 117 ASN cc_start: 0.9203 (p0) cc_final: 0.8925 (p0) REVERT: W 60 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7906 (ptp-170) REVERT: W 77 GLU cc_start: 0.9163 (tp30) cc_final: 0.8926 (tp30) REVERT: W 98 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: W 134 PHE cc_start: 0.8550 (t80) cc_final: 0.8253 (t80) REVERT: X 98 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7427 (m-10) outliers start: 131 outliers final: 73 residues processed: 851 average time/residue: 0.1474 time to fit residues: 200.9127 Evaluate side-chains 826 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 725 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 75 THR Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 245 optimal weight: 10.0000 chunk 208 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 170 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN H 92 GLN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN T 92 GLN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.075716 restraints weight = 47586.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.078324 restraints weight = 22085.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079999 restraints weight = 12394.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.081085 restraints weight = 7954.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081828 restraints weight = 5687.625| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24216 Z= 0.190 Angle : 0.788 14.228 32712 Z= 0.392 Chirality : 0.053 0.341 3648 Planarity : 0.004 0.029 4368 Dihedral : 5.783 26.624 3384 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 6.19 % Allowed : 24.92 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.13), residues: 3168 helix: -1.55 (0.21), residues: 480 sheet: -1.04 (0.15), residues: 936 loop : -2.70 (0.12), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 51 TYR 0.007 0.001 TYR T 112 PHE 0.017 0.002 PHE D 70 TRP 0.011 0.001 TRP X 50 HIS 0.005 0.002 HIS T 116 Details of bonding type rmsd covalent geometry : bond 0.00433 (24216) covalent geometry : angle 0.78792 (32712) hydrogen bonds : bond 0.03879 ( 912) hydrogen bonds : angle 5.01419 ( 2664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 755 time to evaluate : 0.844 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: B 33 SER cc_start: 0.9215 (t) cc_final: 0.8547 (p) REVERT: B 35 ASN cc_start: 0.8522 (m-40) cc_final: 0.8206 (m110) REVERT: B 47 GLN cc_start: 0.8511 (pm20) cc_final: 0.8271 (pm20) REVERT: B 76 ASP cc_start: 0.8337 (t0) cc_final: 0.7969 (t0) REVERT: B 98 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 4 GLN cc_start: 0.8414 (tp40) cc_final: 0.8057 (mm-40) REVERT: A 12 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8603 (mtpp) REVERT: A 28 ARG cc_start: 0.8432 (mtm180) cc_final: 0.7108 (mmp-170) REVERT: A 76 ASP cc_start: 0.7839 (t0) cc_final: 0.7457 (t0) REVERT: A 98 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: A 117 ASN cc_start: 0.9159 (p0) cc_final: 0.8877 (p0) REVERT: C 98 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8055 (m-10) REVERT: C 134 PHE cc_start: 0.8674 (t80) cc_final: 0.8126 (t80) REVERT: D 8 ASP cc_start: 0.7562 (m-30) cc_final: 0.7243 (m-30) REVERT: D 22 GLU cc_start: 0.6749 (mp0) cc_final: 0.6495 (mp0) REVERT: D 45 GLU cc_start: 0.7204 (pm20) cc_final: 0.6897 (pp20) REVERT: D 98 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: D 110 ILE cc_start: 0.9103 (tp) cc_final: 0.8888 (tp) REVERT: E 35 ASN cc_start: 0.8511 (m-40) cc_final: 0.8246 (m110) REVERT: E 76 ASP cc_start: 0.8453 (t0) cc_final: 0.7988 (t0) REVERT: E 90 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: E 98 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: E 134 PHE cc_start: 0.8427 (t80) cc_final: 0.7952 (t80) REVERT: F 4 GLN cc_start: 0.8565 (mm-40) cc_final: 0.7776 (mm-40) REVERT: F 28 ARG cc_start: 0.8567 (mtm180) cc_final: 0.7400 (mmp-170) REVERT: F 90 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8437 (mm-30) REVERT: F 98 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: G 98 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: H 23 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8199 (p) REVERT: H 45 GLU cc_start: 0.7308 (pm20) cc_final: 0.6825 (pp20) REVERT: H 52 GLU cc_start: 0.7039 (mp0) cc_final: 0.6806 (mp0) REVERT: H 98 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: I 35 ASN cc_start: 0.8649 (m-40) cc_final: 0.8272 (m-40) REVERT: I 76 ASP cc_start: 0.8431 (t0) cc_final: 0.7956 (t0) REVERT: I 90 GLU cc_start: 0.8090 (tp30) cc_final: 0.7849 (mm-30) REVERT: I 98 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: J 4 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7920 (mm-40) REVERT: J 28 ARG cc_start: 0.8544 (mtm180) cc_final: 0.7350 (mmp-170) REVERT: J 71 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8923 (mtpp) REVERT: J 98 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: J 117 ASN cc_start: 0.9196 (p0) cc_final: 0.8882 (p0) REVERT: K 98 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8003 (m-10) REVERT: L 45 GLU cc_start: 0.7170 (pm20) cc_final: 0.6779 (pp20) REVERT: L 98 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: L 123 GLU cc_start: 0.7814 (mp0) cc_final: 0.7602 (mp0) REVERT: M 33 SER cc_start: 0.9217 (t) cc_final: 0.8695 (p) REVERT: M 47 GLN cc_start: 0.8533 (pm20) cc_final: 0.8281 (pm20) REVERT: M 76 ASP cc_start: 0.8351 (t0) cc_final: 0.7969 (t0) REVERT: M 92 GLN cc_start: 0.8833 (tt0) cc_final: 0.8273 (tt0) REVERT: M 98 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: N 4 GLN cc_start: 0.8410 (tp40) cc_final: 0.8056 (mm-40) REVERT: N 12 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8607 (mtpp) REVERT: N 28 ARG cc_start: 0.8432 (mtm180) cc_final: 0.7101 (mmp-170) REVERT: N 98 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: N 117 ASN cc_start: 0.9155 (p0) cc_final: 0.8870 (p0) REVERT: O 98 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: O 134 PHE cc_start: 0.8669 (t80) cc_final: 0.8125 (t80) REVERT: P 8 ASP cc_start: 0.7583 (m-30) cc_final: 0.7289 (m-30) REVERT: P 45 GLU cc_start: 0.7231 (pm20) cc_final: 0.6943 (pp20) REVERT: Q 35 ASN cc_start: 0.8459 (m-40) cc_final: 0.8164 (m110) REVERT: Q 76 ASP cc_start: 0.8444 (t0) cc_final: 0.7953 (t0) REVERT: Q 90 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: Q 98 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: Q 134 PHE cc_start: 0.8434 (t80) cc_final: 0.7959 (t80) REVERT: R 4 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7765 (mm-40) REVERT: R 28 ARG cc_start: 0.8568 (mtm180) cc_final: 0.7398 (mmp-170) REVERT: R 90 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8435 (mm-30) REVERT: R 98 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: S 98 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: T 23 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8085 (p) REVERT: T 46 SER cc_start: 0.8271 (m) cc_final: 0.7757 (m) REVERT: T 52 GLU cc_start: 0.6982 (mp0) cc_final: 0.6242 (mp0) REVERT: T 98 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: U 35 ASN cc_start: 0.8640 (m-40) cc_final: 0.8266 (m-40) REVERT: U 76 ASP cc_start: 0.8438 (t0) cc_final: 0.7956 (t0) REVERT: U 90 GLU cc_start: 0.8089 (tp30) cc_final: 0.7859 (mm-30) REVERT: U 98 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: V 4 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7916 (mm-40) REVERT: V 28 ARG cc_start: 0.8485 (mtm180) cc_final: 0.7229 (mmt180) REVERT: V 71 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8925 (mtpp) REVERT: V 98 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: V 117 ASN cc_start: 0.9195 (p0) cc_final: 0.8879 (p0) REVERT: V 126 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7249 (mtm) REVERT: W 98 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: W 134 PHE cc_start: 0.8533 (t80) cc_final: 0.8239 (t80) REVERT: X 45 GLU cc_start: 0.7161 (pm20) cc_final: 0.6761 (pp20) outliers start: 150 outliers final: 87 residues processed: 840 average time/residue: 0.1450 time to fit residues: 195.4016 Evaluate side-chains 817 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 701 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 75 THR Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 237 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.0570 chunk 75 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 35 optimal weight: 0.0070 chunk 93 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 102 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN T 92 GLN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 GLN X 92 GLN ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.077590 restraints weight = 47004.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.080183 restraints weight = 21712.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081843 restraints weight = 12186.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.082959 restraints weight = 7837.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.083687 restraints weight = 5570.570| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24216 Z= 0.160 Angle : 0.795 14.348 32712 Z= 0.390 Chirality : 0.053 0.313 3648 Planarity : 0.004 0.031 4368 Dihedral : 5.625 26.680 3384 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.65 % Allowed : 27.39 % Favored : 66.96 % 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: -2.92 (0.13), residues: 3168 helix: -1.43 (0.21), residues: 480 sheet: -1.00 (0.15), residues: 936 loop : -2.71 (0.12), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 51 TYR 0.009 0.001 TYR E 112 PHE 0.014 0.002 PHE P 70 TRP 0.011 0.001 TRP X 50 HIS 0.008 0.002 HIS T 116 Details of bonding type rmsd covalent geometry : bond 0.00365 (24216) covalent geometry : angle 0.79464 (32712) hydrogen bonds : bond 0.03605 ( 912) hydrogen bonds : angle 4.86428 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 768 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 SER cc_start: 0.9149 (t) cc_final: 0.8525 (p) REVERT: B 35 ASN cc_start: 0.8451 (m-40) cc_final: 0.8152 (m110) REVERT: B 47 GLN cc_start: 0.8481 (pm20) cc_final: 0.8257 (pm20) REVERT: B 76 ASP cc_start: 0.8298 (t0) cc_final: 0.7852 (t0) REVERT: B 98 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: A 4 GLN cc_start: 0.8349 (tp40) cc_final: 0.7974 (mm-40) REVERT: A 12 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (mtpp) REVERT: A 28 ARG cc_start: 0.8319 (mtm180) cc_final: 0.7026 (mmp-170) REVERT: A 76 ASP cc_start: 0.7858 (t0) cc_final: 0.7457 (t0) REVERT: A 117 ASN cc_start: 0.9146 (p0) cc_final: 0.8843 (p0) REVERT: C 98 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: C 134 PHE cc_start: 0.8616 (t80) cc_final: 0.8109 (t80) REVERT: D 22 GLU cc_start: 0.6694 (mp0) cc_final: 0.6466 (mp0) REVERT: D 45 GLU cc_start: 0.7150 (pm20) cc_final: 0.6813 (pp20) REVERT: D 76 ASP cc_start: 0.7823 (t0) cc_final: 0.7596 (t0) REVERT: D 98 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: E 76 ASP cc_start: 0.8409 (t0) cc_final: 0.7940 (t0) REVERT: E 98 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: E 134 PHE cc_start: 0.8334 (t80) cc_final: 0.7847 (t80) REVERT: F 4 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7807 (mm-40) REVERT: F 28 ARG cc_start: 0.8530 (mtm180) cc_final: 0.7460 (mmp-170) REVERT: F 98 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: G 98 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8613 (m-10) REVERT: H 23 THR cc_start: 0.8443 (m) cc_final: 0.8091 (p) REVERT: H 28 ARG cc_start: 0.9064 (mpp80) cc_final: 0.8863 (mpp80) REVERT: H 46 SER cc_start: 0.8283 (m) cc_final: 0.7858 (m) REVERT: H 52 GLU cc_start: 0.7046 (mp0) cc_final: 0.6587 (mp0) REVERT: H 98 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: I 35 ASN cc_start: 0.8610 (m-40) cc_final: 0.8296 (m-40) REVERT: I 47 GLN cc_start: 0.8499 (pm20) cc_final: 0.8169 (pm20) REVERT: I 76 ASP cc_start: 0.8364 (t0) cc_final: 0.7915 (t0) REVERT: I 90 GLU cc_start: 0.8107 (tp30) cc_final: 0.7831 (mm-30) REVERT: I 98 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7304 (m-10) REVERT: J 4 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7909 (mm-40) REVERT: J 28 ARG cc_start: 0.8407 (mtm180) cc_final: 0.7328 (mmp-170) REVERT: J 71 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8913 (mtpp) REVERT: J 98 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: J 100 ILE cc_start: 0.8805 (mm) cc_final: 0.8503 (mm) REVERT: J 117 ASN cc_start: 0.9176 (p0) cc_final: 0.8834 (p0) REVERT: K 98 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7960 (m-10) REVERT: L 45 GLU cc_start: 0.7116 (pm20) cc_final: 0.6674 (pp20) REVERT: L 98 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: L 123 GLU cc_start: 0.7822 (mp0) cc_final: 0.7592 (mp0) REVERT: M 33 SER cc_start: 0.9145 (t) cc_final: 0.8559 (p) REVERT: M 35 ASN cc_start: 0.8512 (m-40) cc_final: 0.8141 (m110) REVERT: M 47 GLN cc_start: 0.8505 (pm20) cc_final: 0.8287 (pm20) REVERT: M 76 ASP cc_start: 0.8311 (t0) cc_final: 0.7844 (t0) REVERT: M 92 GLN cc_start: 0.8834 (tt0) cc_final: 0.8387 (tt0) REVERT: M 98 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: M 134 PHE cc_start: 0.8416 (t80) cc_final: 0.8129 (t80) REVERT: N 4 GLN cc_start: 0.8350 (tp40) cc_final: 0.7972 (mm-40) REVERT: N 12 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8770 (mtpp) REVERT: N 28 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7019 (mmp-170) REVERT: N 117 ASN cc_start: 0.9144 (p0) cc_final: 0.8841 (p0) REVERT: O 98 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: O 110 ILE cc_start: 0.9079 (tp) cc_final: 0.8824 (tp) REVERT: O 134 PHE cc_start: 0.8610 (t80) cc_final: 0.8105 (t80) REVERT: P 45 GLU cc_start: 0.7163 (pm20) cc_final: 0.6849 (pp20) REVERT: P 98 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: Q 35 ASN cc_start: 0.8505 (m-40) cc_final: 0.8245 (m110) REVERT: Q 76 ASP cc_start: 0.8388 (t0) cc_final: 0.7920 (t0) REVERT: Q 90 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: Q 98 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: Q 134 PHE cc_start: 0.8338 (t80) cc_final: 0.7852 (t80) REVERT: R 4 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7801 (mm-40) REVERT: R 28 ARG cc_start: 0.8542 (mtm180) cc_final: 0.7466 (mmp-170) REVERT: R 98 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: S 98 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8580 (m-10) REVERT: T 23 THR cc_start: 0.8324 (m) cc_final: 0.7868 (p) REVERT: T 45 GLU cc_start: 0.7208 (pm20) cc_final: 0.6729 (pp20) REVERT: T 46 SER cc_start: 0.8387 (m) cc_final: 0.7839 (m) REVERT: T 52 GLU cc_start: 0.7009 (mp0) cc_final: 0.6307 (mp0) REVERT: T 98 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7613 (m-10) REVERT: U 35 ASN cc_start: 0.8604 (m-40) cc_final: 0.8282 (m-40) REVERT: U 76 ASP cc_start: 0.8372 (t0) cc_final: 0.7906 (t0) REVERT: U 90 GLU cc_start: 0.8104 (tp30) cc_final: 0.7830 (mm-30) REVERT: U 98 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: V 4 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7912 (mm-40) REVERT: V 28 ARG cc_start: 0.8417 (mtm180) cc_final: 0.7369 (mmp-170) REVERT: V 71 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8915 (mtpp) REVERT: V 98 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: V 100 ILE cc_start: 0.8905 (mm) cc_final: 0.8583 (mm) REVERT: V 117 ASN cc_start: 0.9173 (p0) cc_final: 0.8817 (p0) REVERT: W 98 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: W 134 PHE cc_start: 0.8438 (t80) cc_final: 0.8161 (t80) REVERT: X 45 GLU cc_start: 0.7155 (pm20) cc_final: 0.6694 (pp20) REVERT: X 98 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7792 (m-80) outliers start: 137 outliers final: 82 residues processed: 843 average time/residue: 0.1474 time to fit residues: 199.5604 Evaluate side-chains 822 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 715 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 0.3980 chunk 228 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 GLN ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.085220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.073816 restraints weight = 48311.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.076337 restraints weight = 22795.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.077981 restraints weight = 12990.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.079042 restraints weight = 8438.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079793 restraints weight = 6089.508| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 24216 Z= 0.255 Angle : 0.845 15.216 32712 Z= 0.422 Chirality : 0.055 0.380 3648 Planarity : 0.004 0.051 4368 Dihedral : 5.859 24.902 3384 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.57 % Allowed : 28.51 % Favored : 65.92 % 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: -3.00 (0.13), residues: 3168 helix: -1.43 (0.21), residues: 480 sheet: -1.17 (0.14), residues: 936 loop : -2.72 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.013 0.002 TYR F 122 PHE 0.018 0.002 PHE D 70 TRP 0.011 0.002 TRP X 50 HIS 0.006 0.002 HIS T 116 Details of bonding type rmsd covalent geometry : bond 0.00585 (24216) covalent geometry : angle 0.84475 (32712) hydrogen bonds : bond 0.04017 ( 912) hydrogen bonds : angle 4.96033 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 695 time to evaluate : 0.889 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: B 33 SER cc_start: 0.9143 (t) cc_final: 0.8650 (p) REVERT: B 47 GLN cc_start: 0.8580 (pm20) cc_final: 0.8249 (pm20) REVERT: B 76 ASP cc_start: 0.8499 (t0) cc_final: 0.7967 (t0) REVERT: B 98 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: A 4 GLN cc_start: 0.8382 (tp40) cc_final: 0.8120 (tp40) REVERT: A 12 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8540 (mtpp) REVERT: A 28 ARG cc_start: 0.8555 (mtm180) cc_final: 0.7130 (mmp-170) REVERT: A 76 ASP cc_start: 0.7980 (t0) cc_final: 0.7609 (t0) REVERT: A 98 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: A 117 ASN cc_start: 0.9167 (p0) cc_final: 0.8936 (p0) REVERT: C 98 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8078 (m-10) REVERT: C 110 ILE cc_start: 0.9108 (tp) cc_final: 0.8849 (tp) REVERT: C 134 PHE cc_start: 0.8756 (t80) cc_final: 0.8208 (t80) REVERT: D 22 GLU cc_start: 0.6935 (mp0) cc_final: 0.6628 (mp0) REVERT: D 45 GLU cc_start: 0.7487 (pm20) cc_final: 0.7173 (pp20) REVERT: D 76 ASP cc_start: 0.7949 (t0) cc_final: 0.7735 (t0) REVERT: D 98 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: E 76 ASP cc_start: 0.8564 (t0) cc_final: 0.8041 (t0) REVERT: E 98 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: E 134 PHE cc_start: 0.8418 (t80) cc_final: 0.7965 (t80) REVERT: F 28 ARG cc_start: 0.8618 (mtm180) cc_final: 0.7336 (mmp-170) REVERT: F 98 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: G 98 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8791 (m-80) REVERT: H 23 THR cc_start: 0.8541 (m) cc_final: 0.8158 (p) REVERT: H 52 GLU cc_start: 0.7036 (mp0) cc_final: 0.6779 (mp0) REVERT: H 98 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: H 117 ASN cc_start: 0.9401 (p0) cc_final: 0.9088 (p0) REVERT: I 35 ASN cc_start: 0.8641 (m-40) cc_final: 0.8279 (m-40) REVERT: I 76 ASP cc_start: 0.8557 (t0) cc_final: 0.7895 (t0) REVERT: I 98 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: J 4 GLN cc_start: 0.8633 (mm-40) cc_final: 0.7963 (mm-40) REVERT: J 28 ARG cc_start: 0.8667 (mtm180) cc_final: 0.7274 (mmt180) REVERT: J 71 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8972 (mtpp) REVERT: J 98 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: J 117 ASN cc_start: 0.9154 (p0) cc_final: 0.8882 (p0) REVERT: K 98 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: L 45 GLU cc_start: 0.7500 (pm20) cc_final: 0.7144 (pp20) REVERT: L 98 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: M 33 SER cc_start: 0.9216 (t) cc_final: 0.8834 (p) REVERT: M 47 GLN cc_start: 0.8609 (pm20) cc_final: 0.8272 (pm20) REVERT: M 76 ASP cc_start: 0.8521 (t0) cc_final: 0.8238 (t0) REVERT: M 92 GLN cc_start: 0.8975 (tt0) cc_final: 0.8315 (tt0) REVERT: M 98 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: N 4 GLN cc_start: 0.8391 (tp40) cc_final: 0.8122 (tp40) REVERT: N 12 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8543 (mtpp) REVERT: N 28 ARG cc_start: 0.8547 (mtm180) cc_final: 0.7074 (mmp-170) REVERT: N 98 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: N 117 ASN cc_start: 0.9165 (p0) cc_final: 0.8936 (p0) REVERT: O 98 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: O 110 ILE cc_start: 0.9096 (tp) cc_final: 0.8833 (tp) REVERT: O 134 PHE cc_start: 0.8748 (t80) cc_final: 0.8215 (t80) REVERT: P 8 ASP cc_start: 0.7700 (m-30) cc_final: 0.7365 (m-30) REVERT: P 22 GLU cc_start: 0.7093 (mp0) cc_final: 0.6837 (mp0) REVERT: P 45 GLU cc_start: 0.7420 (pm20) cc_final: 0.7075 (pp20) REVERT: P 98 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7900 (m-10) REVERT: Q 35 ASN cc_start: 0.8600 (m-40) cc_final: 0.8355 (m110) REVERT: Q 76 ASP cc_start: 0.8562 (t0) cc_final: 0.7956 (t0) REVERT: Q 98 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: Q 134 PHE cc_start: 0.8422 (t80) cc_final: 0.7964 (t80) REVERT: R 28 ARG cc_start: 0.8621 (mtm180) cc_final: 0.7339 (mmp-170) REVERT: R 98 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: S 98 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: T 23 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8078 (p) REVERT: T 52 GLU cc_start: 0.7027 (mp0) cc_final: 0.6604 (mp0) REVERT: T 98 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7569 (m-10) REVERT: U 35 ASN cc_start: 0.8625 (m-40) cc_final: 0.8256 (m-40) REVERT: U 76 ASP cc_start: 0.8568 (t0) cc_final: 0.7890 (t0) REVERT: U 98 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: V 4 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7959 (mm-40) REVERT: V 28 ARG cc_start: 0.8671 (mtm180) cc_final: 0.7230 (mmt180) REVERT: V 71 LYS cc_start: 0.9233 (mtpt) cc_final: 0.8975 (mtpp) REVERT: V 98 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: V 117 ASN cc_start: 0.9145 (p0) cc_final: 0.8864 (p0) REVERT: W 98 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: W 134 PHE cc_start: 0.8528 (t80) cc_final: 0.8231 (t80) REVERT: X 45 GLU cc_start: 0.7613 (pm20) cc_final: 0.7242 (pp20) REVERT: X 98 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7735 (m-80) outliers start: 135 outliers final: 86 residues processed: 774 average time/residue: 0.1454 time to fit residues: 182.2934 Evaluate side-chains 791 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 678 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.073465 restraints weight = 48269.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.076009 restraints weight = 22682.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077661 restraints weight = 12857.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078757 restraints weight = 8318.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.079488 restraints weight = 5939.745| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24216 Z= 0.252 Angle : 0.859 15.025 32712 Z= 0.428 Chirality : 0.055 0.384 3648 Planarity : 0.004 0.059 4368 Dihedral : 5.971 27.676 3384 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.07 % Allowed : 29.33 % Favored : 65.59 % 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: -3.08 (0.13), residues: 3168 helix: -1.46 (0.21), residues: 480 sheet: -1.26 (0.14), residues: 936 loop : -2.75 (0.12), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.011 0.001 TYR T 112 PHE 0.015 0.002 PHE P 70 TRP 0.012 0.002 TRP X 50 HIS 0.006 0.002 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00581 (24216) covalent geometry : angle 0.85883 (32712) hydrogen bonds : bond 0.03972 ( 912) hydrogen bonds : angle 5.00283 ( 2664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 698 time to evaluate : 0.855 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: B 33 SER cc_start: 0.9150 (t) cc_final: 0.8641 (p) REVERT: B 47 GLN cc_start: 0.8572 (pm20) cc_final: 0.8298 (pm20) REVERT: B 76 ASP cc_start: 0.8552 (t0) cc_final: 0.7977 (t0) REVERT: B 98 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: A 4 GLN cc_start: 0.8376 (tp40) cc_final: 0.8088 (tp40) REVERT: A 12 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: A 28 ARG cc_start: 0.8565 (mtm180) cc_final: 0.7052 (mmp-170) REVERT: A 76 ASP cc_start: 0.7984 (t0) cc_final: 0.7638 (t0) REVERT: A 117 ASN cc_start: 0.9159 (p0) cc_final: 0.8945 (p0) REVERT: C 98 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8087 (m-10) REVERT: C 110 ILE cc_start: 0.9097 (tp) cc_final: 0.8827 (tp) REVERT: C 134 PHE cc_start: 0.8762 (t80) cc_final: 0.8239 (t80) REVERT: D 22 GLU cc_start: 0.7042 (mp0) cc_final: 0.6716 (mp0) REVERT: D 76 ASP cc_start: 0.7977 (t0) cc_final: 0.7764 (t0) REVERT: D 98 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: E 76 ASP cc_start: 0.8602 (t0) cc_final: 0.8084 (t0) REVERT: E 78 ARG cc_start: 0.8905 (tpt170) cc_final: 0.8633 (tpt-90) REVERT: E 90 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: E 98 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: E 134 PHE cc_start: 0.8407 (t80) cc_final: 0.7977 (t80) REVERT: F 28 ARG cc_start: 0.8629 (mtm180) cc_final: 0.7278 (mmp-170) REVERT: F 98 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: G 98 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8764 (m-80) REVERT: H 23 THR cc_start: 0.8533 (m) cc_final: 0.8091 (p) REVERT: H 52 GLU cc_start: 0.7103 (mp0) cc_final: 0.6794 (mp0) REVERT: H 117 ASN cc_start: 0.9409 (p0) cc_final: 0.9106 (p0) REVERT: I 35 ASN cc_start: 0.8705 (m-40) cc_final: 0.8355 (m-40) REVERT: I 76 ASP cc_start: 0.8550 (t0) cc_final: 0.7893 (t0) REVERT: I 98 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: J 4 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7983 (mm-40) REVERT: J 28 ARG cc_start: 0.8706 (mtm180) cc_final: 0.7276 (mmt180) REVERT: J 71 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8986 (mtpp) REVERT: J 98 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: J 117 ASN cc_start: 0.9152 (p0) cc_final: 0.8911 (p0) REVERT: K 98 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8106 (m-10) REVERT: L 45 GLU cc_start: 0.7636 (pm20) cc_final: 0.7272 (pp20) REVERT: M 31 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8298 (ttm-80) REVERT: M 33 SER cc_start: 0.9159 (t) cc_final: 0.8770 (p) REVERT: M 47 GLN cc_start: 0.8602 (pm20) cc_final: 0.8327 (pm20) REVERT: M 76 ASP cc_start: 0.8553 (t0) cc_final: 0.8222 (t0) REVERT: M 92 GLN cc_start: 0.8963 (tt0) cc_final: 0.8271 (tt0) REVERT: M 98 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: N 4 GLN cc_start: 0.8386 (tp40) cc_final: 0.8093 (tp40) REVERT: N 12 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8424 (mtpp) REVERT: N 28 ARG cc_start: 0.8577 (mtm180) cc_final: 0.7048 (mmp-170) REVERT: N 117 ASN cc_start: 0.9156 (p0) cc_final: 0.8937 (p0) REVERT: O 98 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: O 110 ILE cc_start: 0.9080 (tp) cc_final: 0.8826 (tp) REVERT: O 134 PHE cc_start: 0.8760 (t80) cc_final: 0.8234 (t80) REVERT: P 28 ARG cc_start: 0.8854 (mtm180) cc_final: 0.8593 (mtm180) REVERT: P 98 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: Q 35 ASN cc_start: 0.8579 (m-40) cc_final: 0.8316 (m110) REVERT: Q 76 ASP cc_start: 0.8563 (t0) cc_final: 0.7938 (t0) REVERT: Q 98 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: Q 134 PHE cc_start: 0.8408 (t80) cc_final: 0.7974 (t80) REVERT: R 28 ARG cc_start: 0.8634 (mtm180) cc_final: 0.7307 (mmp-170) REVERT: R 98 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: S 98 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: T 23 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8082 (p) REVERT: T 52 GLU cc_start: 0.7025 (mp0) cc_final: 0.6583 (mp0) REVERT: T 98 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7685 (m-10) REVERT: U 35 ASN cc_start: 0.8685 (m-40) cc_final: 0.8334 (m-40) REVERT: U 76 ASP cc_start: 0.8558 (t0) cc_final: 0.7874 (t0) REVERT: U 98 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: V 4 GLN cc_start: 0.8631 (mm-40) cc_final: 0.7987 (mm-40) REVERT: V 28 ARG cc_start: 0.8682 (mtm180) cc_final: 0.7261 (mmp-170) REVERT: V 71 LYS cc_start: 0.9267 (mtpt) cc_final: 0.8979 (mtpp) REVERT: V 98 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: V 117 ASN cc_start: 0.9167 (p0) cc_final: 0.8918 (p0) REVERT: W 98 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: W 134 PHE cc_start: 0.8506 (t80) cc_final: 0.8201 (t80) REVERT: X 45 GLU cc_start: 0.7706 (pm20) cc_final: 0.7325 (pp20) REVERT: X 98 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7688 (m-80) outliers start: 123 outliers final: 86 residues processed: 774 average time/residue: 0.1466 time to fit residues: 182.7257 Evaluate side-chains 793 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 683 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 291 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.079118 restraints weight = 46606.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.081730 restraints weight = 21687.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.083412 restraints weight = 12188.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.084524 restraints weight = 7827.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.085278 restraints weight = 5567.111| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24216 Z= 0.148 Angle : 0.828 12.675 32712 Z= 0.404 Chirality : 0.053 0.349 3648 Planarity : 0.004 0.033 4368 Dihedral : 5.621 24.837 3384 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.25 % Allowed : 30.69 % Favored : 65.06 % 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: -3.07 (0.12), residues: 3168 helix: -1.44 (0.21), residues: 480 sheet: -1.10 (0.15), residues: 888 loop : -2.82 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.009 0.001 TYR T 112 PHE 0.016 0.002 PHE P 70 TRP 0.010 0.001 TRP L 50 HIS 0.005 0.001 HIS H 116 Details of bonding type rmsd covalent geometry : bond 0.00334 (24216) covalent geometry : angle 0.82844 (32712) hydrogen bonds : bond 0.03504 ( 912) hydrogen bonds : angle 4.86445 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.42 seconds wall clock time: 73 minutes 50.91 seconds (4430.91 seconds total)