Starting phenix.real_space_refine on Sun Aug 24 16:03:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp9_37713/08_2025/8wp9_37713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp9_37713/08_2025/8wp9_37713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wp9_37713/08_2025/8wp9_37713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp9_37713/08_2025/8wp9_37713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wp9_37713/08_2025/8wp9_37713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp9_37713/08_2025/8wp9_37713.map" } resolution = 2.49 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= 0.155 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 13680 2.51 5 N 3528 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21432 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Restraints were copied for chains: P, T, U, E, I, X, D, F, R, O, C, B, W, K, N, H, L, M, Q, J, G, S, V Time building chain proxies: 1.44, per 1000 atoms: 0.07 Number of scatterers: 21432 At special positions: 0 Unit cell: (132.581, 132.581, 132.581, 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 4176 8.00 N 3528 7.00 C 13680 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: 1.71 Conformation dependent library (CDL) restraints added in 749.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 11.3% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE A 140 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA P 120 " --> pdb=" O GLU P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE P 140 " --> pdb=" O GLU P 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 66 No H-bonds generated for 'chain 'T' and resid 64 through 66' Processing helix chain 'T' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA T 120 " --> pdb=" O GLU T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE T 140 " --> pdb=" O GLU T 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 66 No H-bonds generated for 'chain 'U' and resid 64 through 66' Processing helix chain 'U' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA U 120 " --> pdb=" O GLU U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE U 140 " --> pdb=" O GLU U 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE E 140 " --> pdb=" O GLU E 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA I 120 " --> pdb=" O GLU I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE I 140 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA X 120 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE X 140 " --> pdb=" O GLU X 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA D 120 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE D 140 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA F 120 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE F 140 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA R 120 " --> pdb=" O GLU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE R 140 " --> pdb=" O GLU R 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing helix chain 'O' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA O 120 " --> pdb=" O GLU O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE O 140 " --> pdb=" O GLU O 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA C 120 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE C 140 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE B 140 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 66 No H-bonds generated for 'chain 'W' and resid 64 through 66' Processing helix chain 'W' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA W 120 " --> pdb=" O GLU W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE W 140 " --> pdb=" O GLU W 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA K 120 " --> pdb=" O GLU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE K 140 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA N 120 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE N 140 " --> pdb=" O GLU N 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA H 120 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 66 No H-bonds generated for 'chain 'L' and resid 64 through 66' Processing helix chain 'L' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA L 120 " --> pdb=" O GLU L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE L 140 " --> pdb=" O GLU L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 66 No H-bonds generated for 'chain 'M' and resid 64 through 66' Processing helix chain 'M' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA M 120 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE M 140 " --> pdb=" O GLU M 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 66 No H-bonds generated for 'chain 'Q' and resid 64 through 66' Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA Q 120 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE Q 140 " --> pdb=" O GLU Q 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA J 120 " --> pdb=" O GLU J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE J 140 " --> pdb=" O GLU J 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA G 120 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE G 140 " --> pdb=" O GLU G 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA S 120 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE S 140 " --> pdb=" O GLU S 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 66 No H-bonds generated for 'chain 'V' and resid 64 through 66' Processing helix chain 'V' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA V 120 " --> pdb=" O GLU V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE V 140 " --> pdb=" O GLU V 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 146 through 147 removed outlier: 7.786A pdb=" N ALA A 122 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 96 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU A 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE C 94 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 5.633A pdb=" N ILE A 94 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU C 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 96 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA C 122 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.944A pdb=" N PHE B 124 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 96 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU B 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE D 94 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 36 through 40 Processing sheet with id=AA7, first strand: chain 'P' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR O 96 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU P 49 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE O 94 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE P 94 " --> pdb=" O GLU O 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU O 49 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR P 96 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AB1, first strand: chain 'P' and resid 146 through 147 removed outlier: 3.829A pdb=" N PHE G 124 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR H 96 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE H 94 " --> pdb=" O GLU G 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 36 through 40 Processing sheet with id=AB3, first strand: chain 'R' and resid 93 through 97 removed outlier: 5.617A pdb=" N ILE R 94 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU T 49 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 96 " --> pdb=" O ILE T 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA T 122 " --> pdb=" O GLU K 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 93 through 97 removed outlier: 5.526A pdb=" N ILE T 94 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU R 49 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR T 96 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 142 through 143 Processing sheet with id=AB6, first strand: chain 'T' and resid 146 through 147 removed outlier: 4.072A pdb=" N PHE X 124 " --> pdb=" O GLU T 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR W 96 " --> pdb=" O ILE X 47 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU X 49 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE W 94 " --> pdb=" O GLU X 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 36 through 40 Processing sheet with id=AB8, first strand: chain 'F' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE F 94 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU U 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 96 " --> pdb=" O ILE U 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA U 122 " --> pdb=" O GLU V 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE U 94 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 49 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR U 96 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA F 122 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 142 through 143 Processing sheet with id=AC2, first strand: chain 'U' and resid 146 through 147 removed outlier: 3.712A pdb=" N PHE Q 124 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR S 96 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU Q 49 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE S 94 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 147 removed outlier: 7.830A pdb=" N ALA E 122 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR N 96 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU E 49 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE N 94 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE E 94 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU N 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR E 96 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 36 through 40 Processing sheet with id=AC7, first strand: chain 'I' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR K 96 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU I 49 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE K 94 " --> pdb=" O GLU I 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE I 94 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU K 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR I 96 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE K 124 " --> pdb=" O GLU O 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 142 through 143 Processing sheet with id=AD1, first strand: chain 'I' and resid 146 through 147 removed outlier: 3.760A pdb=" N PHE J 124 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR L 96 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU J 49 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE L 94 " --> pdb=" O GLU J 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 93 through 97 removed outlier: 5.567A pdb=" N ILE X 94 " --> pdb=" O GLU W 49 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU W 49 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR X 96 " --> pdb=" O ILE W 47 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA W 122 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 142 through 143 Processing sheet with id=AD4, first strand: chain 'D' and resid 36 through 40 Processing sheet with id=AD5, first strand: chain 'B' and resid 93 through 97 removed outlier: 5.750A pdb=" N ILE B 94 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU D 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 96 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA D 122 " --> pdb=" O GLU S 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AD7, first strand: chain 'F' and resid 36 through 40 Processing sheet with id=AD8, first strand: chain 'R' and resid 36 through 40 Processing sheet with id=AD9, first strand: chain 'R' and resid 142 through 143 Processing sheet with id=AE1, first strand: chain 'R' and resid 146 through 147 removed outlier: 4.058A pdb=" N PHE V 124 " --> pdb=" O GLU R 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 96 " --> pdb=" O ILE V 47 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU V 49 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE M 94 " --> pdb=" O GLU V 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 40 Processing sheet with id=AE4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE5, first strand: chain 'W' and resid 36 through 40 Processing sheet with id=AE6, first strand: chain 'W' and resid 142 through 143 Processing sheet with id=AE7, first strand: chain 'N' and resid 36 through 40 Processing sheet with id=AE8, first strand: chain 'N' and resid 142 through 143 Processing sheet with id=AE9, first strand: chain 'N' and resid 146 through 147 removed outlier: 3.723A pdb=" N PHE M 124 " --> pdb=" O GLU N 147 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR V 96 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU M 49 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE V 94 " --> pdb=" O GLU M 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR G 96 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE G 94 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.635A pdb=" N TYR J 96 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU L 49 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE J 94 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 93 through 97 removed outlier: 5.581A pdb=" N ILE Q 94 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU S 49 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2331 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: 2.82 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6907 1.34 - 1.46: 1738 1.46 - 1.57: 12979 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 21720 Sorted by residual: bond pdb=" CA ILE X 45 " pdb=" CB ILE X 45 " ideal model delta sigma weight residual 1.544 1.570 -0.026 1.42e-02 4.96e+03 3.26e+00 bond pdb=" CA ILE D 45 " pdb=" CB ILE D 45 " ideal model delta sigma weight residual 1.544 1.570 -0.026 1.42e-02 4.96e+03 3.24e+00 bond pdb=" CA ILE T 45 " pdb=" CB ILE T 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.21e+00 bond pdb=" CA ILE Q 45 " pdb=" CB ILE Q 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.18e+00 bond pdb=" CA ILE L 45 " pdb=" CB ILE L 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.17e+00 ... (remaining 21715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 26911 1.45 - 2.90: 1870 2.90 - 4.34: 306 4.34 - 5.79: 164 5.79 - 7.24: 53 Bond angle restraints: 29304 Sorted by residual: angle pdb=" CA GLU V 101 " pdb=" CB GLU V 101 " pdb=" CG GLU V 101 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU T 101 " pdb=" CB GLU T 101 " pdb=" CG GLU T 101 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA GLU X 101 " pdb=" CB GLU X 101 " pdb=" CG GLU X 101 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA GLU J 101 " pdb=" CB GLU J 101 " pdb=" CG GLU J 101 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 ... (remaining 29299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 12126 17.73 - 35.45: 1266 35.45 - 53.18: 144 53.18 - 70.91: 24 70.91 - 88.63: 48 Dihedral angle restraints: 13608 sinusoidal: 5688 harmonic: 7920 Sorted by residual: dihedral pdb=" CB GLU I 49 " pdb=" CG GLU I 49 " pdb=" CD GLU I 49 " pdb=" OE1 GLU I 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 dihedral pdb=" CB GLU N 49 " pdb=" CG GLU N 49 " pdb=" CD GLU N 49 " pdb=" OE1 GLU N 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 dihedral pdb=" CB GLU O 49 " pdb=" CG GLU O 49 " pdb=" CD GLU O 49 " pdb=" OE1 GLU O 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 ... (remaining 13605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1506 0.033 - 0.066: 1096 0.066 - 0.099: 410 0.099 - 0.132: 348 0.132 - 0.166: 120 Chirality restraints: 3480 Sorted by residual: chirality pdb=" CA ILE P 35 " pdb=" N ILE P 35 " pdb=" C ILE P 35 " pdb=" CB ILE P 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE B 35 " pdb=" N ILE B 35 " pdb=" C ILE B 35 " pdb=" CB ILE B 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE G 35 " pdb=" N ILE G 35 " pdb=" C ILE G 35 " pdb=" CB ILE G 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 3477 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU W 133 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO W 134 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO W 134 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO W 134 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 133 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO C 134 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 133 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO Q 134 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO Q 134 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO Q 134 " -0.019 5.00e-02 4.00e+02 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5552 2.83 - 3.35: 15205 3.35 - 3.87: 31265 3.87 - 4.38: 35621 4.38 - 4.90: 67567 Nonbonded interactions: 155210 Sorted by model distance: nonbonded pdb=" OE1 GLU D 78 " pdb=" OG1 THR D 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU C 78 " pdb=" OG1 THR C 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU M 78 " pdb=" OG1 THR M 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU L 78 " pdb=" OG1 THR L 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU R 78 " pdb=" OG1 THR R 108 " model vdw 2.315 3.040 ... (remaining 155205 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'E' selection = chain 'I' selection = chain 'X' selection = chain 'D' selection = chain 'F' selection = chain 'R' selection = chain 'O' selection = chain 'C' selection = chain 'B' selection = chain 'W' selection = chain 'K' selection = chain 'N' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'J' selection = chain 'G' selection = chain 'S' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 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: 0.030 Process input model: 14.030 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21720 Z= 0.261 Angle : 0.949 7.239 29304 Z= 0.532 Chirality : 0.061 0.166 3480 Planarity : 0.006 0.034 3720 Dihedral : 15.191 88.632 8472 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.00 % Allowed : 4.00 % Favored : 95.00 % 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 aren not related in a simple way. whole: 1.51 (0.16), residues: 2712 helix: None (None), residues: 0 sheet: 3.06 (0.15), residues: 1392 loop : -1.54 (0.12), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 93 TYR 0.012 0.003 TYR M 106 PHE 0.005 0.001 PHE R 42 TRP 0.002 0.001 TRP O 59 HIS 0.002 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00531 (21720) covalent geometry : angle 0.94904 (29304) hydrogen bonds : bond 0.16049 ( 945) hydrogen bonds : angle 4.24944 ( 2331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 807 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: X 147 GLU cc_start: 0.6990 (pp20) cc_final: 0.6717 (pp20) REVERT: D 98 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 147 GLU cc_start: 0.5987 (pp20) cc_final: 0.5740 (pp20) outliers start: 24 outliers final: 0 residues processed: 824 average time/residue: 0.6814 time to fit residues: 617.8886 Evaluate side-chains 475 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 119 ASN P 36 GLN P 119 ASN T 36 GLN T 119 ASN T 126 ASN U 36 GLN U 119 ASN E 36 GLN I 36 GLN I 119 ASN X 53 HIS X 119 ASN F 53 HIS R 36 GLN O 53 HIS C 36 GLN B 53 HIS W 36 GLN K 36 GLN N 36 GLN N 119 ASN H 36 GLN L 36 GLN L 145 ASN M 36 GLN M 119 ASN Q 53 HIS Q 119 ASN J 36 GLN G 53 HIS S 36 GLN V 36 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104055 restraints weight = 23351.964| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.13 r_work: 0.3000 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.7587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 21720 Z= 0.259 Angle : 0.830 9.912 29304 Z= 0.427 Chirality : 0.058 0.161 3480 Planarity : 0.005 0.040 3720 Dihedral : 5.137 17.087 2880 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.04 % Allowed : 19.71 % Favored : 75.25 % 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 aren not related in a simple way. whole: 1.83 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.05 (0.15), residues: 1392 loop : -1.03 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 93 TYR 0.008 0.002 TYR M 96 PHE 0.009 0.002 PHE W 124 TRP 0.005 0.001 TRP E 59 HIS 0.008 0.002 HIS O 53 Details of bonding type rmsd covalent geometry : bond 0.00654 (21720) covalent geometry : angle 0.82966 (29304) hydrogen bonds : bond 0.05606 ( 945) hydrogen bonds : angle 4.16637 ( 2331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 634 time to evaluate : 0.956 Fit side-chains REVERT: A 87 MET cc_start: 0.7654 (pmm) cc_final: 0.7330 (mmt) REVERT: A 101 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: A 102 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: A 123 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8476 (mttp) REVERT: A 142 LYS cc_start: 0.8231 (mttm) cc_final: 0.7848 (mptt) REVERT: P 87 MET cc_start: 0.7603 (pmm) cc_final: 0.7295 (mmp) REVERT: P 101 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: P 123 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8446 (mttp) REVERT: P 142 LYS cc_start: 0.8227 (mttm) cc_final: 0.7849 (mptt) REVERT: T 87 MET cc_start: 0.7661 (pmm) cc_final: 0.7323 (mmt) REVERT: T 101 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: T 123 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8423 (mttp) REVERT: T 142 LYS cc_start: 0.8215 (mttm) cc_final: 0.7857 (mptt) REVERT: U 87 MET cc_start: 0.7602 (pmm) cc_final: 0.7302 (mmp) REVERT: U 101 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: U 123 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8456 (mttp) REVERT: U 142 LYS cc_start: 0.8194 (mttm) cc_final: 0.7815 (mptt) REVERT: E 78 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: E 102 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: E 104 GLU cc_start: 0.7701 (tp30) cc_final: 0.7386 (mm-30) REVERT: I 123 LYS cc_start: 0.8632 (pttt) cc_final: 0.8183 (mttt) REVERT: I 142 LYS cc_start: 0.8263 (mmtt) cc_final: 0.8013 (mptt) REVERT: X 49 GLU cc_start: 0.8590 (tt0) cc_final: 0.8387 (tt0) REVERT: X 92 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: X 101 GLU cc_start: 0.7958 (mp0) cc_final: 0.7596 (mm-30) REVERT: X 142 LYS cc_start: 0.8214 (mttm) cc_final: 0.7914 (mptt) REVERT: D 36 GLN cc_start: 0.8348 (mt0) cc_final: 0.8107 (mt0) REVERT: D 78 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: D 110 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8298 (tttm) REVERT: D 116 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8509 (mtmt) REVERT: D 142 LYS cc_start: 0.8285 (mttm) cc_final: 0.7949 (mptt) REVERT: F 49 GLU cc_start: 0.8611 (tt0) cc_final: 0.8370 (tt0) REVERT: F 78 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: F 103 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: F 110 LYS cc_start: 0.8853 (tttm) cc_final: 0.8415 (ttpt) REVERT: F 118 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: R 49 GLU cc_start: 0.8614 (tt0) cc_final: 0.8382 (tt0) REVERT: R 78 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: R 103 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: R 110 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8384 (tttm) REVERT: R 118 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: O 49 GLU cc_start: 0.8614 (tt0) cc_final: 0.8373 (tt0) REVERT: O 78 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: O 103 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: O 110 LYS cc_start: 0.8855 (tttm) cc_final: 0.8411 (ttpt) REVERT: O 118 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: C 78 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: C 93 ARG cc_start: 0.8570 (pmt170) cc_final: 0.8321 (pmt170) REVERT: C 101 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: C 110 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8362 (tttm) REVERT: C 118 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 49 GLU cc_start: 0.8632 (tt0) cc_final: 0.8410 (tt0) REVERT: B 101 GLU cc_start: 0.7981 (mp0) cc_final: 0.7556 (mm-30) REVERT: B 142 LYS cc_start: 0.8307 (mttm) cc_final: 0.7991 (mptt) REVERT: W 78 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: W 87 MET cc_start: 0.7331 (pmt) cc_final: 0.7044 (mmt) REVERT: W 103 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7598 (tm-30) REVERT: W 110 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8339 (tttm) REVERT: W 125 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: K 78 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: K 102 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: K 104 GLU cc_start: 0.7693 (tp30) cc_final: 0.7379 (mm-30) REVERT: N 123 LYS cc_start: 0.8638 (pttt) cc_final: 0.8190 (mttt) REVERT: N 142 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8003 (mptt) REVERT: H 78 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: H 87 MET cc_start: 0.7536 (mmm) cc_final: 0.7326 (mmt) REVERT: H 103 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7544 (tm-30) REVERT: H 110 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8319 (ttpt) REVERT: H 142 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7956 (mptt) REVERT: L 78 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: L 102 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: L 104 GLU cc_start: 0.7684 (tp30) cc_final: 0.7392 (mm-30) REVERT: M 82 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7913 (ptpt) REVERT: M 101 GLU cc_start: 0.7898 (mp0) cc_final: 0.7110 (mm-30) REVERT: Q 92 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: Q 101 GLU cc_start: 0.7971 (mp0) cc_final: 0.7648 (mm-30) REVERT: Q 142 LYS cc_start: 0.8263 (mttm) cc_final: 0.7950 (mptt) REVERT: J 101 GLU cc_start: 0.7844 (mp0) cc_final: 0.7049 (mm-30) REVERT: G 101 GLU cc_start: 0.7969 (mp0) cc_final: 0.7577 (mm-30) REVERT: G 142 LYS cc_start: 0.8289 (mttm) cc_final: 0.7981 (mptt) REVERT: S 78 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: S 93 ARG cc_start: 0.8392 (pmt170) cc_final: 0.7932 (pmt170) REVERT: S 110 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8340 (ttpt) REVERT: S 116 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8536 (mtmt) REVERT: S 142 LYS cc_start: 0.8116 (mttp) cc_final: 0.7877 (mptt) REVERT: V 49 GLU cc_start: 0.8735 (tt0) cc_final: 0.8485 (tt0) REVERT: V 78 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8330 (tm-30) outliers start: 121 outliers final: 26 residues processed: 703 average time/residue: 0.7570 time to fit residues: 583.4574 Evaluate side-chains 603 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 543 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 101 GLU Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 78 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 110 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 53 HIS X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 53 HIS B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 53 HIS Q 119 ASN J 119 ASN G 53 HIS G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108464 restraints weight = 24052.158| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.22 r_work: 0.3143 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.7655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21720 Z= 0.180 Angle : 0.693 9.481 29304 Z= 0.350 Chirality : 0.054 0.152 3480 Planarity : 0.004 0.034 3720 Dihedral : 4.621 15.324 2880 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.58 % Allowed : 21.12 % Favored : 74.29 % 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 aren not related in a simple way. whole: 2.04 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.08 (0.15), residues: 1392 loop : -0.75 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 93 TYR 0.008 0.002 TYR S 106 PHE 0.006 0.001 PHE J 124 TRP 0.003 0.001 TRP A 59 HIS 0.006 0.002 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00447 (21720) covalent geometry : angle 0.69297 (29304) hydrogen bonds : bond 0.04837 ( 945) hydrogen bonds : angle 3.91492 ( 2331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 571 time to evaluate : 1.129 Fit side-chains REVERT: A 101 GLU cc_start: 0.7833 (mp0) cc_final: 0.7246 (mm-30) REVERT: A 103 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: A 123 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8398 (mttt) REVERT: A 142 LYS cc_start: 0.8256 (mttm) cc_final: 0.7979 (mptt) REVERT: P 49 GLU cc_start: 0.8658 (tt0) cc_final: 0.8458 (tt0) REVERT: P 87 MET cc_start: 0.7582 (pmm) cc_final: 0.7357 (mmt) REVERT: P 101 GLU cc_start: 0.7840 (mp0) cc_final: 0.7206 (mm-30) REVERT: P 123 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8341 (mttp) REVERT: P 142 LYS cc_start: 0.8218 (mttm) cc_final: 0.7948 (mptt) REVERT: T 87 MET cc_start: 0.7575 (pmm) cc_final: 0.7346 (mmt) REVERT: T 101 GLU cc_start: 0.7896 (mp0) cc_final: 0.7263 (mm-30) REVERT: T 103 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: T 123 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8353 (mttp) REVERT: T 142 LYS cc_start: 0.8288 (mttm) cc_final: 0.7956 (mptt) REVERT: U 87 MET cc_start: 0.7598 (pmm) cc_final: 0.7361 (mmt) REVERT: U 101 GLU cc_start: 0.7822 (mp0) cc_final: 0.7176 (mm-30) REVERT: U 123 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8363 (mttp) REVERT: U 142 LYS cc_start: 0.8254 (mttm) cc_final: 0.7984 (mptt) REVERT: E 78 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: E 102 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: E 103 GLU cc_start: 0.7857 (tp30) cc_final: 0.7588 (tm-30) REVERT: E 104 GLU cc_start: 0.7651 (tp30) cc_final: 0.7441 (mm-30) REVERT: I 101 GLU cc_start: 0.7899 (mp0) cc_final: 0.7293 (mm-30) REVERT: X 87 MET cc_start: 0.7380 (pmm) cc_final: 0.7036 (mmt) REVERT: X 92 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: X 101 GLU cc_start: 0.7905 (mp0) cc_final: 0.7658 (mm-30) REVERT: X 142 LYS cc_start: 0.8218 (mttm) cc_final: 0.7909 (mptt) REVERT: D 78 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: D 87 MET cc_start: 0.7216 (pmt) cc_final: 0.7010 (mmt) REVERT: D 91 SER cc_start: 0.5418 (OUTLIER) cc_final: 0.5154 (t) REVERT: D 110 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8434 (ttpt) REVERT: D 142 LYS cc_start: 0.8261 (mttm) cc_final: 0.7921 (mptt) REVERT: F 49 GLU cc_start: 0.8632 (tt0) cc_final: 0.8396 (tt0) REVERT: F 78 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: F 110 LYS cc_start: 0.8864 (tttm) cc_final: 0.8488 (ttpt) REVERT: F 118 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: R 78 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: R 110 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8433 (tttm) REVERT: R 118 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: O 49 GLU cc_start: 0.8626 (tt0) cc_final: 0.8392 (tt0) REVERT: O 78 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: O 110 LYS cc_start: 0.8851 (tttm) cc_final: 0.8497 (ttpt) REVERT: O 118 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: C 49 GLU cc_start: 0.8559 (tt0) cc_final: 0.8332 (tt0) REVERT: C 78 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: C 110 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8440 (ttpt) REVERT: C 118 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 87 MET cc_start: 0.7389 (pmm) cc_final: 0.7073 (mmt) REVERT: B 101 GLU cc_start: 0.7934 (mp0) cc_final: 0.7595 (mm-30) REVERT: B 142 LYS cc_start: 0.8293 (mttm) cc_final: 0.7969 (mptt) REVERT: W 78 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: W 91 SER cc_start: 0.5474 (OUTLIER) cc_final: 0.5221 (t) REVERT: W 103 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7511 (tm-30) REVERT: W 110 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8344 (tttm) REVERT: W 125 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: K 78 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: K 102 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: K 103 GLU cc_start: 0.7831 (tp30) cc_final: 0.7564 (tm-30) REVERT: K 104 GLU cc_start: 0.7637 (tp30) cc_final: 0.7425 (mm-30) REVERT: N 101 GLU cc_start: 0.7907 (mp0) cc_final: 0.7282 (mm-30) REVERT: H 46 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8861 (m) REVERT: H 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: H 87 MET cc_start: 0.7669 (mmm) cc_final: 0.7466 (mmt) REVERT: H 91 SER cc_start: 0.5467 (OUTLIER) cc_final: 0.5230 (t) REVERT: H 103 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7498 (tm-30) REVERT: H 110 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8312 (tttm) REVERT: L 78 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: L 102 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: L 104 GLU cc_start: 0.7674 (tp30) cc_final: 0.7443 (mm-30) REVERT: M 101 GLU cc_start: 0.7975 (mp0) cc_final: 0.7327 (mm-30) REVERT: M 110 LYS cc_start: 0.8902 (tttm) cc_final: 0.8640 (tttm) REVERT: Q 87 MET cc_start: 0.7363 (pmm) cc_final: 0.7029 (mmt) REVERT: Q 92 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: Q 142 LYS cc_start: 0.8288 (mttm) cc_final: 0.7972 (mptt) REVERT: J 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: J 101 GLU cc_start: 0.7931 (mp0) cc_final: 0.7263 (mm-30) REVERT: J 103 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8115 (mt-10) REVERT: G 87 MET cc_start: 0.7389 (pmm) cc_final: 0.7079 (mmt) REVERT: G 101 GLU cc_start: 0.7934 (mp0) cc_final: 0.7606 (mm-30) REVERT: G 142 LYS cc_start: 0.8289 (mttm) cc_final: 0.7967 (mptt) REVERT: S 78 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: S 103 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7535 (tm-30) REVERT: S 110 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8317 (tttm) REVERT: V 78 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: V 104 GLU cc_start: 0.7677 (tp30) cc_final: 0.7458 (mm-30) outliers start: 110 outliers final: 41 residues processed: 641 average time/residue: 0.8540 time to fit residues: 601.5210 Evaluate side-chains 620 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 548 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 174 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107687 restraints weight = 24002.865| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.21 r_work: 0.3131 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.7773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 21720 Z= 0.183 Angle : 0.688 9.218 29304 Z= 0.347 Chirality : 0.054 0.154 3480 Planarity : 0.004 0.035 3720 Dihedral : 4.558 15.014 2880 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.29 % Allowed : 21.83 % Favored : 72.88 % 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 aren not related in a simple way. whole: 2.08 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.08 (0.15), residues: 1392 loop : -0.67 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 80 TYR 0.009 0.002 TYR E 106 PHE 0.007 0.001 PHE J 124 TRP 0.003 0.001 TRP Q 59 HIS 0.004 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00457 (21720) covalent geometry : angle 0.68841 (29304) hydrogen bonds : bond 0.04839 ( 945) hydrogen bonds : angle 3.92489 ( 2331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 557 time to evaluate : 0.886 Fit side-chains REVERT: A 37 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8639 (mm) REVERT: A 78 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: A 101 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: A 123 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8398 (mttt) REVERT: A 142 LYS cc_start: 0.8267 (mttm) cc_final: 0.7935 (mptt) REVERT: P 78 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: P 87 MET cc_start: 0.7577 (pmm) cc_final: 0.7355 (mmt) REVERT: P 101 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: P 103 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: P 123 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8349 (mttp) REVERT: P 142 LYS cc_start: 0.8246 (mttm) cc_final: 0.7918 (mptt) REVERT: T 78 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: T 87 MET cc_start: 0.7540 (pmm) cc_final: 0.7335 (mmt) REVERT: T 101 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: T 123 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8363 (mttp) REVERT: T 142 LYS cc_start: 0.8290 (mttm) cc_final: 0.7975 (mptt) REVERT: U 78 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: U 87 MET cc_start: 0.7591 (pmm) cc_final: 0.7353 (mmt) REVERT: U 101 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: U 103 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: U 123 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8353 (mttp) REVERT: U 142 LYS cc_start: 0.8270 (mttm) cc_final: 0.7946 (mptt) REVERT: E 102 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: E 104 GLU cc_start: 0.7641 (tp30) cc_final: 0.7384 (mm-30) REVERT: I 49 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: I 101 GLU cc_start: 0.7873 (mp0) cc_final: 0.7396 (mm-30) REVERT: I 102 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: X 87 MET cc_start: 0.7426 (pmm) cc_final: 0.7118 (mmt) REVERT: X 92 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: X 101 GLU cc_start: 0.7945 (mp0) cc_final: 0.7676 (mm-30) REVERT: X 142 LYS cc_start: 0.8253 (mttm) cc_final: 0.7931 (mptt) REVERT: D 78 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: D 87 MET cc_start: 0.7316 (pmt) cc_final: 0.7114 (mmt) REVERT: D 91 SER cc_start: 0.5367 (OUTLIER) cc_final: 0.5140 (t) REVERT: D 103 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7549 (tm-30) REVERT: D 110 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8395 (tttm) REVERT: D 142 LYS cc_start: 0.8243 (mttm) cc_final: 0.7911 (mptt) REVERT: F 78 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: F 110 LYS cc_start: 0.8865 (tttm) cc_final: 0.8476 (ttpt) REVERT: F 118 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: R 78 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: R 110 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8440 (tttm) REVERT: R 118 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: O 78 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: O 110 LYS cc_start: 0.8870 (tttm) cc_final: 0.8488 (ttpt) REVERT: O 118 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: C 78 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: C 110 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8389 (tttm) REVERT: C 118 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: B 87 MET cc_start: 0.7496 (pmm) cc_final: 0.7253 (mmt) REVERT: B 101 GLU cc_start: 0.7932 (mp0) cc_final: 0.7619 (mm-30) REVERT: B 142 LYS cc_start: 0.8348 (mttm) cc_final: 0.8003 (mptt) REVERT: W 78 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: W 91 SER cc_start: 0.5313 (OUTLIER) cc_final: 0.5088 (t) REVERT: W 103 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7429 (tm-30) REVERT: W 110 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8384 (tttm) REVERT: W 125 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: K 102 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: K 104 GLU cc_start: 0.7640 (tp30) cc_final: 0.7384 (mm-30) REVERT: N 49 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: N 101 GLU cc_start: 0.7888 (mp0) cc_final: 0.7394 (mm-30) REVERT: N 102 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: H 78 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: H 87 MET cc_start: 0.7734 (mmm) cc_final: 0.7512 (mmt) REVERT: H 91 SER cc_start: 0.5405 (OUTLIER) cc_final: 0.5192 (t) REVERT: H 103 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7432 (tm-30) REVERT: H 110 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8351 (tttm) REVERT: L 78 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: L 104 GLU cc_start: 0.7641 (tp30) cc_final: 0.7365 (mm-30) REVERT: M 101 GLU cc_start: 0.7987 (mp0) cc_final: 0.7473 (mm-30) REVERT: Q 87 MET cc_start: 0.7410 (pmm) cc_final: 0.7102 (mmt) REVERT: Q 92 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: Q 142 LYS cc_start: 0.8336 (mttm) cc_final: 0.8016 (mptt) REVERT: J 78 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: J 82 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7961 (ptpt) REVERT: J 101 GLU cc_start: 0.7969 (mp0) cc_final: 0.7365 (mm-30) REVERT: J 102 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: G 87 MET cc_start: 0.7462 (pmm) cc_final: 0.7246 (mmt) REVERT: G 101 GLU cc_start: 0.7908 (mp0) cc_final: 0.7626 (mm-30) REVERT: G 142 LYS cc_start: 0.8342 (mttm) cc_final: 0.8003 (mptt) REVERT: S 78 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: S 91 SER cc_start: 0.5421 (OUTLIER) cc_final: 0.5195 (t) REVERT: S 103 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7509 (tm-30) REVERT: S 110 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8382 (tttm) REVERT: V 78 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: V 104 GLU cc_start: 0.7679 (tp30) cc_final: 0.7439 (mm-30) outliers start: 127 outliers final: 46 residues processed: 640 average time/residue: 0.7386 time to fit residues: 522.6672 Evaluate side-chains 638 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 550 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 101 GLU Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain O residue 145 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 209 optimal weight: 0.0270 chunk 194 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109942 restraints weight = 23773.615| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.20 r_work: 0.3095 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.7809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 21720 Z= 0.091 Angle : 0.530 8.069 29304 Z= 0.266 Chirality : 0.051 0.146 3480 Planarity : 0.003 0.024 3720 Dihedral : 3.803 12.721 2880 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.62 % Allowed : 23.79 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.17 (0.15), residues: 1392 loop : -0.34 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 107 TYR 0.008 0.001 TYR J 106 PHE 0.004 0.001 PHE J 124 TRP 0.002 0.000 TRP E 59 HIS 0.004 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00200 (21720) covalent geometry : angle 0.53010 (29304) hydrogen bonds : bond 0.03440 ( 945) hydrogen bonds : angle 3.70744 ( 2331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 574 time to evaluate : 0.799 Fit side-chains REVERT: A 78 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: A 101 GLU cc_start: 0.7688 (mp0) cc_final: 0.7177 (mm-30) REVERT: A 123 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8328 (mttt) REVERT: A 142 LYS cc_start: 0.8063 (mttm) cc_final: 0.7736 (mptt) REVERT: P 49 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: P 78 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: P 87 MET cc_start: 0.7560 (pmm) cc_final: 0.7276 (mmt) REVERT: P 101 GLU cc_start: 0.7674 (mp0) cc_final: 0.7135 (mm-30) REVERT: P 103 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: P 123 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8292 (mttt) REVERT: P 142 LYS cc_start: 0.8032 (mttm) cc_final: 0.7710 (mptt) REVERT: T 78 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: T 87 MET cc_start: 0.7512 (pmm) cc_final: 0.7264 (mmt) REVERT: T 101 GLU cc_start: 0.7802 (mp0) cc_final: 0.7240 (mm-30) REVERT: T 123 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8288 (mttt) REVERT: T 142 LYS cc_start: 0.8096 (mttm) cc_final: 0.7785 (mptt) REVERT: U 78 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: U 87 MET cc_start: 0.7545 (pmm) cc_final: 0.7276 (mmt) REVERT: U 101 GLU cc_start: 0.7702 (mp0) cc_final: 0.7130 (mm-30) REVERT: U 103 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: U 123 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8298 (mttt) REVERT: U 142 LYS cc_start: 0.8033 (mttm) cc_final: 0.7712 (mptt) REVERT: E 49 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: E 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: E 104 GLU cc_start: 0.7545 (tp30) cc_final: 0.7334 (mm-30) REVERT: E 110 LYS cc_start: 0.8841 (tttm) cc_final: 0.8564 (tttm) REVERT: I 101 GLU cc_start: 0.7849 (mp0) cc_final: 0.7274 (mm-30) REVERT: I 102 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: X 87 MET cc_start: 0.7350 (pmm) cc_final: 0.6979 (mmt) REVERT: X 101 GLU cc_start: 0.7899 (mp0) cc_final: 0.7556 (mm-30) REVERT: X 142 LYS cc_start: 0.8045 (mttm) cc_final: 0.7729 (mptt) REVERT: D 110 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8113 (tttm) REVERT: D 142 LYS cc_start: 0.8016 (mttm) cc_final: 0.7668 (mptt) REVERT: F 110 LYS cc_start: 0.8779 (tttm) cc_final: 0.8350 (ttpt) REVERT: F 118 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: R 110 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8356 (ttpt) REVERT: R 118 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: O 110 LYS cc_start: 0.8758 (tttm) cc_final: 0.8346 (ttpt) REVERT: O 118 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: C 101 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: C 110 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8342 (ttpt) REVERT: C 118 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 87 MET cc_start: 0.7399 (pmm) cc_final: 0.7040 (mmt) REVERT: B 101 GLU cc_start: 0.7931 (mp0) cc_final: 0.7536 (mm-30) REVERT: B 142 LYS cc_start: 0.8099 (mttm) cc_final: 0.7820 (mptt) REVERT: W 78 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: W 103 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7203 (tm-30) REVERT: W 110 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8142 (tttm) REVERT: W 125 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: K 49 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: K 78 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: K 104 GLU cc_start: 0.7548 (tp30) cc_final: 0.7337 (mm-30) REVERT: K 110 LYS cc_start: 0.8822 (tttm) cc_final: 0.8529 (tttm) REVERT: N 101 GLU cc_start: 0.7864 (mp0) cc_final: 0.7272 (mm-30) REVERT: N 102 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: H 78 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: H 87 MET cc_start: 0.7665 (mmm) cc_final: 0.7443 (mmt) REVERT: H 103 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7153 (tm-30) REVERT: H 110 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8116 (tttm) REVERT: L 104 GLU cc_start: 0.7503 (tp30) cc_final: 0.7294 (mm-30) REVERT: L 110 LYS cc_start: 0.8842 (tttm) cc_final: 0.8568 (tttm) REVERT: M 101 GLU cc_start: 0.7951 (mp0) cc_final: 0.7374 (mm-30) REVERT: M 102 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: M 110 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8397 (tttm) REVERT: M 142 LYS cc_start: 0.8018 (mptt) cc_final: 0.7806 (mptt) REVERT: Q 87 MET cc_start: 0.7315 (pmm) cc_final: 0.6923 (mmt) REVERT: Q 142 LYS cc_start: 0.8050 (mttm) cc_final: 0.7777 (mptt) REVERT: J 101 GLU cc_start: 0.7924 (mp0) cc_final: 0.7266 (mm-30) REVERT: J 102 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: J 103 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8014 (mt-10) REVERT: G 87 MET cc_start: 0.7361 (pmm) cc_final: 0.7024 (mmt) REVERT: G 101 GLU cc_start: 0.7927 (mp0) cc_final: 0.7553 (mm-30) REVERT: G 142 LYS cc_start: 0.8061 (mttm) cc_final: 0.7796 (mptt) REVERT: S 78 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: S 103 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7185 (tm-30) REVERT: S 110 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8088 (tttm) REVERT: V 78 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: V 104 GLU cc_start: 0.7605 (tp30) cc_final: 0.7343 (mm-30) REVERT: V 110 LYS cc_start: 0.8856 (tttm) cc_final: 0.8588 (tttm) outliers start: 87 outliers final: 42 residues processed: 628 average time/residue: 0.6974 time to fit residues: 485.4487 Evaluate side-chains 624 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 555 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 247 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105593 restraints weight = 23611.628| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.21 r_work: 0.3025 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.7779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 21720 Z= 0.162 Angle : 0.643 8.901 29304 Z= 0.323 Chirality : 0.053 0.147 3480 Planarity : 0.004 0.035 3720 Dihedral : 4.245 13.423 2880 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.50 % Allowed : 23.29 % Favored : 72.21 % 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 aren not related in a simple way. whole: 2.26 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.10 (0.15), residues: 1392 loop : -0.43 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 80 TYR 0.009 0.002 TYR N 106 PHE 0.006 0.001 PHE M 124 TRP 0.003 0.001 TRP V 59 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00399 (21720) covalent geometry : angle 0.64347 (29304) hydrogen bonds : bond 0.04385 ( 945) hydrogen bonds : angle 3.88297 ( 2331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 561 time to evaluate : 0.621 Fit side-chains REVERT: A 37 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 78 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: A 101 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: A 123 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8422 (mttp) REVERT: A 142 LYS cc_start: 0.8235 (mttm) cc_final: 0.7908 (mptt) REVERT: P 78 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: P 87 MET cc_start: 0.7576 (pmm) cc_final: 0.7317 (mmt) REVERT: P 101 GLU cc_start: 0.7802 (mp0) cc_final: 0.7279 (mm-30) REVERT: P 103 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: P 123 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8361 (mttt) REVERT: P 142 LYS cc_start: 0.8210 (mttm) cc_final: 0.7891 (mptt) REVERT: T 78 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: T 101 GLU cc_start: 0.7888 (mp0) cc_final: 0.7352 (mm-30) REVERT: T 123 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8382 (mttp) REVERT: T 142 LYS cc_start: 0.8248 (mttm) cc_final: 0.7942 (mptt) REVERT: U 78 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: U 87 MET cc_start: 0.7562 (pmm) cc_final: 0.7310 (mmt) REVERT: U 101 GLU cc_start: 0.7827 (mp0) cc_final: 0.7291 (mm-30) REVERT: U 103 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: U 123 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8359 (mttt) REVERT: U 142 LYS cc_start: 0.8218 (mttm) cc_final: 0.7905 (mptt) REVERT: E 49 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: E 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: E 102 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: E 104 GLU cc_start: 0.7604 (tp30) cc_final: 0.7327 (mm-30) REVERT: I 101 GLU cc_start: 0.7957 (mp0) cc_final: 0.7480 (mm-30) REVERT: I 102 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: X 87 MET cc_start: 0.7457 (pmm) cc_final: 0.7100 (mmt) REVERT: X 92 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: X 101 GLU cc_start: 0.7964 (mp0) cc_final: 0.7627 (mm-30) REVERT: X 142 LYS cc_start: 0.8221 (mttm) cc_final: 0.7915 (mptt) REVERT: D 78 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: D 110 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8427 (ttpt) REVERT: D 142 LYS cc_start: 0.8204 (mttm) cc_final: 0.7878 (mptt) REVERT: F 78 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: F 110 LYS cc_start: 0.8873 (tttm) cc_final: 0.8432 (ttpt) REVERT: F 118 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: R 78 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: R 110 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8473 (ttpt) REVERT: R 118 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: O 78 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: O 110 LYS cc_start: 0.8875 (tttm) cc_final: 0.8436 (ttpt) REVERT: O 118 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: C 49 GLU cc_start: 0.8589 (tt0) cc_final: 0.8363 (tt0) REVERT: C 78 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: C 110 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8459 (ttpt) REVERT: C 118 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: B 87 MET cc_start: 0.7474 (pmm) cc_final: 0.7173 (mmt) REVERT: B 101 GLU cc_start: 0.7940 (mp0) cc_final: 0.7581 (mm-30) REVERT: B 142 LYS cc_start: 0.8310 (mttm) cc_final: 0.7962 (mptt) REVERT: W 78 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: W 102 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: W 103 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7324 (tm-30) REVERT: W 110 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8271 (tttm) REVERT: W 125 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: K 49 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: K 78 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: K 102 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: K 104 GLU cc_start: 0.7604 (tp30) cc_final: 0.7330 (mm-30) REVERT: K 110 LYS cc_start: 0.8906 (tttm) cc_final: 0.8612 (tttm) REVERT: N 101 GLU cc_start: 0.7974 (mp0) cc_final: 0.7483 (mm-30) REVERT: N 102 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: H 78 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: H 87 MET cc_start: 0.7760 (mmm) cc_final: 0.7523 (mmt) REVERT: H 103 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7310 (tm-30) REVERT: H 110 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8221 (tttm) REVERT: L 49 GLU cc_start: 0.8578 (tt0) cc_final: 0.8339 (tt0) REVERT: L 78 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: L 104 GLU cc_start: 0.7585 (tp30) cc_final: 0.7327 (mm-30) REVERT: M 101 GLU cc_start: 0.7982 (mp0) cc_final: 0.7471 (mm-30) REVERT: M 102 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: Q 87 MET cc_start: 0.7409 (pmm) cc_final: 0.7062 (mmt) REVERT: Q 142 LYS cc_start: 0.8302 (mttm) cc_final: 0.7971 (mptt) REVERT: J 78 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: J 101 GLU cc_start: 0.7967 (mp0) cc_final: 0.7437 (mm-30) REVERT: J 102 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: J 103 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8083 (mt-10) REVERT: G 87 MET cc_start: 0.7446 (pmm) cc_final: 0.7147 (mmt) REVERT: G 101 GLU cc_start: 0.7945 (mp0) cc_final: 0.7604 (mm-30) REVERT: G 142 LYS cc_start: 0.8310 (mttm) cc_final: 0.7978 (mptt) REVERT: S 78 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: S 91 SER cc_start: 0.5400 (OUTLIER) cc_final: 0.5195 (t) REVERT: S 102 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: S 103 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7315 (tm-30) REVERT: S 110 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8236 (tttm) REVERT: V 78 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: V 104 GLU cc_start: 0.7673 (tp30) cc_final: 0.7397 (mm-30) outliers start: 108 outliers final: 42 residues processed: 628 average time/residue: 0.7206 time to fit residues: 499.5216 Evaluate side-chains 640 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 558 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 167 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110062 restraints weight = 23378.604| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.20 r_work: 0.3116 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 21720 Z= 0.092 Angle : 0.526 8.097 29304 Z= 0.264 Chirality : 0.051 0.143 3480 Planarity : 0.003 0.023 3720 Dihedral : 3.721 12.772 2880 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.21 % Allowed : 24.46 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.14 (0.15), residues: 1392 loop : -0.12 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 93 TYR 0.008 0.001 TYR O 106 PHE 0.004 0.001 PHE J 124 TRP 0.002 0.000 TRP S 59 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00204 (21720) covalent geometry : angle 0.52640 (29304) hydrogen bonds : bond 0.03341 ( 945) hydrogen bonds : angle 3.72570 ( 2331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 538 time to evaluate : 0.602 Fit side-chains REVERT: A 49 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: A 101 GLU cc_start: 0.7727 (mp0) cc_final: 0.7277 (mm-30) REVERT: A 123 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8387 (mttt) REVERT: A 142 LYS cc_start: 0.8091 (mttm) cc_final: 0.7788 (mptt) REVERT: P 78 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: P 87 MET cc_start: 0.7553 (pmm) cc_final: 0.7268 (mmt) REVERT: P 101 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: P 103 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: P 123 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8362 (mttt) REVERT: P 142 LYS cc_start: 0.8060 (mttm) cc_final: 0.7756 (mptt) REVERT: T 78 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: T 101 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: T 123 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8343 (mttt) REVERT: T 142 LYS cc_start: 0.8116 (mttm) cc_final: 0.7839 (mptt) REVERT: U 78 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: U 87 MET cc_start: 0.7567 (pmm) cc_final: 0.7266 (mmt) REVERT: U 101 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: U 103 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: U 123 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8357 (mttt) REVERT: U 142 LYS cc_start: 0.8091 (mttm) cc_final: 0.7788 (mptt) REVERT: E 78 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: E 102 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7190 (mt-10) REVERT: E 110 LYS cc_start: 0.8892 (tttm) cc_final: 0.8629 (tttm) REVERT: I 101 GLU cc_start: 0.7889 (mp0) cc_final: 0.7439 (mm-30) REVERT: I 102 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: X 87 MET cc_start: 0.7385 (pmm) cc_final: 0.7000 (mmt) REVERT: X 92 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: X 101 GLU cc_start: 0.7911 (mp0) cc_final: 0.7571 (mm-30) REVERT: X 142 LYS cc_start: 0.8071 (mttm) cc_final: 0.7792 (mptt) REVERT: D 49 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: D 78 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: D 110 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8178 (tttm) REVERT: D 142 LYS cc_start: 0.8068 (mttm) cc_final: 0.7737 (mptt) REVERT: F 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: F 110 LYS cc_start: 0.8807 (tttm) cc_final: 0.8415 (ttpt) REVERT: F 118 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: R 78 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: R 110 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8408 (ttpt) REVERT: R 118 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: O 78 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: O 110 LYS cc_start: 0.8776 (tttm) cc_final: 0.8396 (ttpt) REVERT: O 118 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: C 49 GLU cc_start: 0.8544 (tt0) cc_final: 0.8299 (tt0) REVERT: C 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: C 101 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: C 110 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8422 (ttpt) REVERT: C 118 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: B 87 MET cc_start: 0.7403 (pmm) cc_final: 0.7053 (mmt) REVERT: B 101 GLU cc_start: 0.7917 (mp0) cc_final: 0.7556 (mm-30) REVERT: B 142 LYS cc_start: 0.8137 (mttm) cc_final: 0.7876 (mptt) REVERT: W 78 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: W 103 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7184 (tm-30) REVERT: W 110 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8201 (tttm) REVERT: W 125 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: K 49 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: K 78 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: K 102 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: K 110 LYS cc_start: 0.8859 (tttm) cc_final: 0.8562 (tttm) REVERT: N 101 GLU cc_start: 0.7884 (mp0) cc_final: 0.7433 (mm-30) REVERT: N 102 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: H 49 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: H 78 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: H 87 MET cc_start: 0.7699 (mmm) cc_final: 0.7471 (mmt) REVERT: H 103 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7187 (tm-30) REVERT: H 110 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8159 (tttm) REVERT: L 49 GLU cc_start: 0.8501 (tt0) cc_final: 0.8256 (tt0) REVERT: L 104 GLU cc_start: 0.7518 (tp30) cc_final: 0.7290 (mm-30) REVERT: L 110 LYS cc_start: 0.8906 (tttm) cc_final: 0.8643 (tttm) REVERT: M 49 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: M 101 GLU cc_start: 0.7920 (mp0) cc_final: 0.7420 (mm-30) REVERT: M 102 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: Q 87 MET cc_start: 0.7350 (pmm) cc_final: 0.6959 (mmt) REVERT: Q 142 LYS cc_start: 0.8123 (mttm) cc_final: 0.7869 (mptt) REVERT: J 78 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: J 101 GLU cc_start: 0.7901 (mp0) cc_final: 0.7402 (mm-30) REVERT: J 102 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: G 87 MET cc_start: 0.7387 (pmm) cc_final: 0.7034 (mmt) REVERT: G 101 GLU cc_start: 0.7908 (mp0) cc_final: 0.7581 (mm-30) REVERT: G 142 LYS cc_start: 0.8125 (mttm) cc_final: 0.7885 (mptt) REVERT: S 78 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: S 103 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7205 (tm-30) REVERT: S 110 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8167 (tttm) REVERT: V 78 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: V 104 GLU cc_start: 0.7589 (tp30) cc_final: 0.7380 (mm-30) REVERT: V 110 LYS cc_start: 0.8907 (tttm) cc_final: 0.8645 (tttm) outliers start: 101 outliers final: 43 residues processed: 595 average time/residue: 0.6947 time to fit residues: 456.4968 Evaluate side-chains 621 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 538 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 101 GLU Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 145 ASN Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 194 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 101 optimal weight: 0.0370 chunk 195 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 252 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105261 restraints weight = 23312.502| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.25 r_work: 0.3015 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 21720 Z= 0.153 Angle : 0.631 8.890 29304 Z= 0.317 Chirality : 0.053 0.146 3480 Planarity : 0.004 0.039 3720 Dihedral : 4.141 13.386 2880 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.67 % Allowed : 24.62 % Favored : 70.71 % 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 aren not related in a simple way. whole: 2.35 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.28 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 93 TYR 0.009 0.002 TYR E 106 PHE 0.006 0.001 PHE N 124 TRP 0.002 0.001 TRP S 59 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00375 (21720) covalent geometry : angle 0.63149 (29304) hydrogen bonds : bond 0.04243 ( 945) hydrogen bonds : angle 3.86496 ( 2331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 559 time to evaluate : 0.673 Fit side-chains REVERT: A 49 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: A 78 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: A 101 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: A 123 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8374 (mttt) REVERT: A 142 LYS cc_start: 0.8199 (mttm) cc_final: 0.7874 (mptt) REVERT: P 78 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: P 87 MET cc_start: 0.7555 (pmm) cc_final: 0.7294 (mmt) REVERT: P 101 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: P 103 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: P 123 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8376 (mttt) REVERT: P 142 LYS cc_start: 0.8176 (mttm) cc_final: 0.7854 (mptt) REVERT: T 78 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: T 101 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: T 123 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8352 (mttt) REVERT: T 142 LYS cc_start: 0.8209 (mttm) cc_final: 0.7910 (mptt) REVERT: U 78 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: U 87 MET cc_start: 0.7558 (pmm) cc_final: 0.7289 (mmt) REVERT: U 101 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: U 103 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: U 123 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8372 (mttt) REVERT: U 142 LYS cc_start: 0.8181 (mttm) cc_final: 0.7858 (mptt) REVERT: E 78 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: E 102 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: E 110 LYS cc_start: 0.8921 (tttm) cc_final: 0.8647 (tttm) REVERT: I 101 GLU cc_start: 0.7940 (mp0) cc_final: 0.7482 (mm-30) REVERT: I 102 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: X 87 MET cc_start: 0.7423 (pmm) cc_final: 0.7089 (mmt) REVERT: X 92 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: X 101 GLU cc_start: 0.7946 (mp0) cc_final: 0.7582 (mm-30) REVERT: X 142 LYS cc_start: 0.8193 (mttm) cc_final: 0.7872 (mptt) REVERT: D 49 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: D 78 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: D 110 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8379 (ttpt) REVERT: D 142 LYS cc_start: 0.8176 (mttm) cc_final: 0.7837 (mptt) REVERT: F 49 GLU cc_start: 0.8479 (tt0) cc_final: 0.8266 (tt0) REVERT: F 78 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: F 110 LYS cc_start: 0.8849 (tttm) cc_final: 0.8405 (ttpt) REVERT: F 118 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: R 78 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: R 110 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8416 (ttpt) REVERT: R 118 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: O 49 GLU cc_start: 0.8486 (tt0) cc_final: 0.8275 (tt0) REVERT: O 78 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: O 110 LYS cc_start: 0.8839 (tttm) cc_final: 0.8406 (ttpt) REVERT: O 118 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: C 49 GLU cc_start: 0.8575 (tt0) cc_final: 0.8340 (tt0) REVERT: C 78 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8253 (tm-30) REVERT: C 101 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: C 110 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8416 (ttpt) REVERT: C 118 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: B 87 MET cc_start: 0.7445 (pmm) cc_final: 0.7101 (mmt) REVERT: B 101 GLU cc_start: 0.7944 (mp0) cc_final: 0.7578 (mm-30) REVERT: B 142 LYS cc_start: 0.8274 (mttm) cc_final: 0.7938 (mptt) REVERT: W 78 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: W 103 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7403 (tm-30) REVERT: W 110 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8210 (tttm) REVERT: W 125 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: K 49 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: K 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: K 102 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: K 110 LYS cc_start: 0.8882 (tttm) cc_final: 0.8572 (tttm) REVERT: N 101 GLU cc_start: 0.7919 (mp0) cc_final: 0.7473 (mm-30) REVERT: N 102 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: H 49 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: H 78 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: H 87 MET cc_start: 0.7773 (mmm) cc_final: 0.7541 (mmt) REVERT: H 102 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: H 103 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7427 (tm-30) REVERT: H 110 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8177 (tttm) REVERT: L 49 GLU cc_start: 0.8554 (tt0) cc_final: 0.8297 (tt0) REVERT: L 78 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: L 104 GLU cc_start: 0.7537 (tp30) cc_final: 0.7322 (mm-30) REVERT: L 110 LYS cc_start: 0.8925 (tttm) cc_final: 0.8652 (tttm) REVERT: M 49 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: M 101 GLU cc_start: 0.7933 (mp0) cc_final: 0.7477 (mm-30) REVERT: M 102 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: Q 49 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: Q 87 MET cc_start: 0.7403 (pmm) cc_final: 0.7038 (mmt) REVERT: Q 142 LYS cc_start: 0.8240 (mttm) cc_final: 0.7929 (mptt) REVERT: J 78 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: J 101 GLU cc_start: 0.7890 (mp0) cc_final: 0.7376 (mm-30) REVERT: J 103 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8104 (mt-10) REVERT: G 87 MET cc_start: 0.7403 (pmm) cc_final: 0.7094 (mmt) REVERT: G 101 GLU cc_start: 0.7927 (mp0) cc_final: 0.7594 (mm-30) REVERT: G 142 LYS cc_start: 0.8241 (mttm) cc_final: 0.7924 (mptt) REVERT: S 78 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: S 103 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7305 (tm-30) REVERT: S 110 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8348 (ttpt) REVERT: V 78 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: V 104 GLU cc_start: 0.7605 (tp30) cc_final: 0.7395 (mm-30) REVERT: V 110 LYS cc_start: 0.8923 (tttm) cc_final: 0.8651 (tttm) outliers start: 112 outliers final: 56 residues processed: 629 average time/residue: 0.7210 time to fit residues: 501.5759 Evaluate side-chains 660 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 560 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 101 GLU Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 234 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 176 optimal weight: 0.0870 chunk 232 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 205 optimal weight: 0.0970 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110663 restraints weight = 23312.863| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.15 r_work: 0.3110 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.7892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 21720 Z= 0.076 Angle : 0.495 7.586 29304 Z= 0.247 Chirality : 0.051 0.138 3480 Planarity : 0.003 0.022 3720 Dihedral : 3.468 12.244 2880 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.04 % Allowed : 26.25 % Favored : 70.71 % 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 aren not related in a simple way. whole: 2.66 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.16 (0.15), residues: 1392 loop : 0.11 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 107 TYR 0.009 0.001 TYR J 106 PHE 0.003 0.000 PHE M 124 TRP 0.001 0.000 TRP T 59 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00163 (21720) covalent geometry : angle 0.49454 (29304) hydrogen bonds : bond 0.03024 ( 945) hydrogen bonds : angle 3.68163 ( 2331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 544 time to evaluate : 0.862 Fit side-chains REVERT: A 78 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: A 101 GLU cc_start: 0.7723 (mp0) cc_final: 0.7312 (mm-30) REVERT: A 123 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8374 (mttt) REVERT: A 142 LYS cc_start: 0.8005 (mttm) cc_final: 0.7733 (mptt) REVERT: P 78 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: P 87 MET cc_start: 0.7486 (pmm) cc_final: 0.7198 (mmt) REVERT: P 101 GLU cc_start: 0.7713 (mp0) cc_final: 0.7197 (mm-30) REVERT: P 103 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: P 123 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8321 (mttt) REVERT: P 142 LYS cc_start: 0.7968 (mttm) cc_final: 0.7690 (mptt) REVERT: T 78 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: T 101 GLU cc_start: 0.7797 (mp0) cc_final: 0.7298 (mm-30) REVERT: T 123 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8322 (mttt) REVERT: T 142 LYS cc_start: 0.8027 (mttm) cc_final: 0.7753 (mptt) REVERT: U 78 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: U 87 MET cc_start: 0.7495 (pmm) cc_final: 0.7180 (mmt) REVERT: U 101 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: U 103 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: U 123 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8324 (mttt) REVERT: U 142 LYS cc_start: 0.7963 (mttm) cc_final: 0.7680 (mptt) REVERT: E 78 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: E 110 LYS cc_start: 0.8842 (tttm) cc_final: 0.8569 (tttm) REVERT: I 101 GLU cc_start: 0.7871 (mp0) cc_final: 0.7410 (mm-30) REVERT: X 87 MET cc_start: 0.7308 (pmm) cc_final: 0.6931 (mmt) REVERT: X 92 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: X 101 GLU cc_start: 0.7830 (mp0) cc_final: 0.7473 (mm-30) REVERT: X 142 LYS cc_start: 0.7971 (mttm) cc_final: 0.7704 (mptt) REVERT: D 78 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: D 110 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8103 (tttm) REVERT: D 142 LYS cc_start: 0.8011 (mttm) cc_final: 0.7703 (mptt) REVERT: F 78 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: F 101 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: F 110 LYS cc_start: 0.8760 (tttm) cc_final: 0.8355 (ttpt) REVERT: F 118 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: R 78 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: R 101 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: R 110 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8342 (ttpt) REVERT: R 118 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: O 78 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: O 101 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: O 110 LYS cc_start: 0.8762 (tttm) cc_final: 0.8377 (ttpt) REVERT: O 118 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: C 78 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: C 101 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: C 110 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8342 (ttpt) REVERT: C 118 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: B 87 MET cc_start: 0.7372 (pmm) cc_final: 0.6947 (mmt) REVERT: B 101 GLU cc_start: 0.7869 (mp0) cc_final: 0.7525 (mm-30) REVERT: B 142 LYS cc_start: 0.8038 (mttm) cc_final: 0.7791 (mptt) REVERT: W 78 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: W 103 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7170 (tm-30) REVERT: W 110 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8116 (tttm) REVERT: W 125 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: K 78 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: K 110 LYS cc_start: 0.8807 (tttm) cc_final: 0.8496 (tttm) REVERT: N 101 GLU cc_start: 0.7859 (mp0) cc_final: 0.7396 (mm-30) REVERT: H 78 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: H 87 MET cc_start: 0.7590 (mmm) cc_final: 0.7363 (mmt) REVERT: H 103 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7125 (tm-30) REVERT: H 110 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8112 (tttm) REVERT: L 49 GLU cc_start: 0.8491 (tt0) cc_final: 0.8223 (tt0) REVERT: L 78 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: L 110 LYS cc_start: 0.8870 (tttm) cc_final: 0.8601 (tttm) REVERT: M 101 GLU cc_start: 0.7901 (mp0) cc_final: 0.7420 (mm-30) REVERT: Q 87 MET cc_start: 0.7288 (pmm) cc_final: 0.6832 (mmt) REVERT: Q 142 LYS cc_start: 0.8010 (mttm) cc_final: 0.7760 (mptt) REVERT: J 78 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: J 101 GLU cc_start: 0.7852 (mp0) cc_final: 0.7351 (mm-30) REVERT: J 102 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: G 87 MET cc_start: 0.7305 (pmm) cc_final: 0.6912 (mmt) REVERT: G 101 GLU cc_start: 0.7848 (mp0) cc_final: 0.7540 (mm-30) REVERT: G 142 LYS cc_start: 0.8023 (mttm) cc_final: 0.7785 (mptt) REVERT: S 78 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: S 103 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7133 (tm-30) REVERT: S 110 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8101 (tttm) REVERT: V 78 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: V 110 LYS cc_start: 0.8882 (tttm) cc_final: 0.8613 (tttm) outliers start: 73 outliers final: 35 residues processed: 589 average time/residue: 0.6843 time to fit residues: 446.5792 Evaluate side-chains 595 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 527 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 54 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 242 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103639 restraints weight = 22797.571| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.19 r_work: 0.3001 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.7833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 21720 Z= 0.188 Angle : 0.680 9.233 29304 Z= 0.342 Chirality : 0.054 0.145 3480 Planarity : 0.004 0.041 3720 Dihedral : 4.244 13.551 2880 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.83 % Allowed : 27.88 % Favored : 69.29 % 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 aren not related in a simple way. whole: 2.37 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.25 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 93 TYR 0.012 0.002 TYR S 106 PHE 0.006 0.001 PHE J 124 TRP 0.003 0.001 TRP G 59 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00475 (21720) covalent geometry : angle 0.68020 (29304) hydrogen bonds : bond 0.04590 ( 945) hydrogen bonds : angle 3.91128 ( 2331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 565 time to evaluate : 0.665 Fit side-chains REVERT: A 78 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: A 101 GLU cc_start: 0.7777 (mp0) cc_final: 0.7418 (mm-30) REVERT: A 123 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8369 (mttp) REVERT: A 142 LYS cc_start: 0.8254 (mttm) cc_final: 0.7917 (mptt) REVERT: P 78 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: P 87 MET cc_start: 0.7508 (pmm) cc_final: 0.7248 (mmt) REVERT: P 101 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: P 103 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: P 123 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8338 (mttt) REVERT: P 142 LYS cc_start: 0.8178 (mttm) cc_final: 0.7837 (mptt) REVERT: T 78 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: T 101 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: T 123 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8333 (mttt) REVERT: T 142 LYS cc_start: 0.8249 (mttm) cc_final: 0.7920 (mptt) REVERT: U 78 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: U 87 MET cc_start: 0.7492 (pmm) cc_final: 0.7237 (mmt) REVERT: U 101 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: U 103 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: U 123 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8324 (mttt) REVERT: U 142 LYS cc_start: 0.8172 (mttm) cc_final: 0.7826 (mptt) REVERT: E 78 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: E 110 LYS cc_start: 0.8865 (tttm) cc_final: 0.8581 (tttm) REVERT: I 101 GLU cc_start: 0.7872 (mp0) cc_final: 0.7478 (mm-30) REVERT: X 87 MET cc_start: 0.7425 (pmm) cc_final: 0.7107 (mmt) REVERT: X 92 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: X 101 GLU cc_start: 0.7917 (mp0) cc_final: 0.7587 (mm-30) REVERT: X 142 LYS cc_start: 0.8189 (mttm) cc_final: 0.7839 (mptt) REVERT: D 78 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: D 110 LYS cc_start: 0.8986 (ttmt) cc_final: 0.8145 (tttm) REVERT: D 142 LYS cc_start: 0.8201 (mttm) cc_final: 0.7838 (mptt) REVERT: F 78 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: F 110 LYS cc_start: 0.8824 (tttm) cc_final: 0.8328 (ttpt) REVERT: F 118 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: R 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: R 110 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8380 (ttpt) REVERT: R 118 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: O 78 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: O 110 LYS cc_start: 0.8832 (tttm) cc_final: 0.8348 (ttpt) REVERT: O 118 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: C 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: C 101 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: C 110 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8376 (ttpt) REVERT: C 118 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: B 87 MET cc_start: 0.7449 (pmm) cc_final: 0.7116 (mmt) REVERT: B 101 GLU cc_start: 0.7898 (mp0) cc_final: 0.7570 (mm-30) REVERT: B 142 LYS cc_start: 0.8292 (mttm) cc_final: 0.7927 (mptt) REVERT: W 78 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: W 103 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7349 (tm-30) REVERT: W 110 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8168 (tttm) REVERT: W 125 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: K 78 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: K 110 LYS cc_start: 0.8835 (tttm) cc_final: 0.8518 (tttm) REVERT: N 101 GLU cc_start: 0.7883 (mp0) cc_final: 0.7473 (mm-30) REVERT: H 78 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: H 87 MET cc_start: 0.7656 (mmm) cc_final: 0.7414 (mmt) REVERT: H 103 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7394 (tm-30) REVERT: H 110 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8112 (tttm) REVERT: L 49 GLU cc_start: 0.8563 (tt0) cc_final: 0.8309 (tt0) REVERT: L 78 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: L 110 LYS cc_start: 0.8902 (tttm) cc_final: 0.8623 (tttm) REVERT: M 101 GLU cc_start: 0.7940 (mp0) cc_final: 0.7459 (mm-30) REVERT: Q 87 MET cc_start: 0.7372 (pmm) cc_final: 0.6989 (mmt) REVERT: Q 142 LYS cc_start: 0.8256 (mttm) cc_final: 0.7897 (mptt) REVERT: J 78 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: J 101 GLU cc_start: 0.7870 (mp0) cc_final: 0.7407 (mm-30) REVERT: J 103 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8083 (mt-10) REVERT: G 87 MET cc_start: 0.7416 (pmm) cc_final: 0.7076 (mmt) REVERT: G 101 GLU cc_start: 0.7868 (mp0) cc_final: 0.7586 (mm-30) REVERT: G 142 LYS cc_start: 0.8269 (mttm) cc_final: 0.7905 (mptt) REVERT: S 78 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: S 102 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: S 103 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7316 (tm-30) REVERT: S 110 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8285 (ttpt) REVERT: V 78 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: V 110 LYS cc_start: 0.8899 (tttm) cc_final: 0.8621 (tttm) outliers start: 68 outliers final: 37 residues processed: 615 average time/residue: 0.7230 time to fit residues: 491.2314 Evaluate side-chains 628 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 559 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 101 GLU Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 181 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 130 optimal weight: 0.0970 chunk 127 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107754 restraints weight = 22884.250| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.18 r_work: 0.3065 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 21720 Z= 0.093 Angle : 0.542 8.085 29304 Z= 0.271 Chirality : 0.051 0.142 3480 Planarity : 0.003 0.023 3720 Dihedral : 3.700 12.804 2880 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.58 % Allowed : 28.33 % Favored : 69.08 % 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 aren not related in a simple way. whole: 2.55 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.12 (0.15), residues: 1392 loop : -0.01 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 107 TYR 0.007 0.001 TYR X 106 PHE 0.004 0.001 PHE N 124 TRP 0.001 0.000 TRP S 59 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00207 (21720) covalent geometry : angle 0.54235 (29304) hydrogen bonds : bond 0.03390 ( 945) hydrogen bonds : angle 3.71756 ( 2331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10608.87 seconds wall clock time: 180 minutes 8.69 seconds (10808.69 seconds total)