Starting phenix.real_space_refine on Wed May 21 08:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp9_37713/05_2025/8wp9_37713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp9_37713/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wp9_37713/05_2025/8wp9_37713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp9_37713/05_2025/8wp9_37713.map" model { file = "/net/cci-nas-00/data/ceres_data/8wp9_37713/05_2025/8wp9_37713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp9_37713/05_2025/8wp9_37713.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 5.44, per 1000 atoms: 0.25 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: 4.76 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 3.99 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: 7.10 Time building geometry restraints manager: 5.60 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 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 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 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.730 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: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 39.900 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.001 TRP O 59 HIS 0.002 0.001 HIS C 53 PHE 0.005 0.001 PHE R 42 TYR 0.012 0.003 TYR M 106 ARG 0.002 0.001 ARG L 93 Details of bonding type rmsd hydrogen bonds : bond 0.16049 ( 945) hydrogen bonds : angle 4.24944 ( 2331) covalent geometry : bond 0.00531 (21720) covalent geometry : angle 0.94904 (29304) *********************** 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 : 2.544 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: 1.6260 time to fit residues: 1476.9469 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 : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 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 J 119 ASN 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 = 0.3585 r_free = 0.3585 target = 0.135703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109457 restraints weight = 23735.774| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.24 r_work: 0.3084 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21720 Z= 0.180 Angle : 0.722 8.905 29304 Z= 0.369 Chirality : 0.055 0.152 3480 Planarity : 0.005 0.033 3720 Dihedral : 4.736 16.071 2880 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.67 % Allowed : 20.38 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.93 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 59 HIS 0.007 0.001 HIS O 53 PHE 0.011 0.001 PHE X 124 TYR 0.008 0.002 TYR R 96 ARG 0.003 0.001 ARG P 107 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 945) hydrogen bonds : angle 4.06888 ( 2331) covalent geometry : bond 0.00427 (21720) covalent geometry : angle 0.72228 (29304) *********************** 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 759 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 647 time to evaluate : 2.703 Fit side-chains REVERT: A 87 MET cc_start: 0.7590 (pmm) cc_final: 0.7160 (mmp) REVERT: A 93 ARG cc_start: 0.8546 (pmt170) cc_final: 0.8212 (pmt170) REVERT: A 101 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: A 102 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: A 123 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8359 (mttp) REVERT: A 142 LYS cc_start: 0.8129 (mttm) cc_final: 0.7780 (mptt) REVERT: P 87 MET cc_start: 0.7575 (pmm) cc_final: 0.7216 (mmp) REVERT: P 123 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8354 (mttt) REVERT: P 142 LYS cc_start: 0.8130 (mttm) cc_final: 0.7782 (mptt) REVERT: T 87 MET cc_start: 0.7581 (pmm) cc_final: 0.7155 (mmp) REVERT: T 101 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7046 (mm-30) REVERT: T 123 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8316 (mttt) REVERT: T 142 LYS cc_start: 0.8083 (mttm) cc_final: 0.7777 (mptt) REVERT: U 87 MET cc_start: 0.7578 (pmm) cc_final: 0.7216 (mmp) REVERT: U 123 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8354 (mttt) REVERT: U 142 LYS cc_start: 0.8070 (mttm) cc_final: 0.7735 (mptt) REVERT: E 49 GLU cc_start: 0.8690 (tt0) cc_final: 0.8415 (tt0) REVERT: E 78 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: E 82 LYS cc_start: 0.8186 (mttm) cc_final: 0.7918 (mtpt) REVERT: E 102 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: E 104 GLU cc_start: 0.7571 (tp30) cc_final: 0.7300 (mm-30) REVERT: I 103 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: I 123 LYS cc_start: 0.8604 (pttt) cc_final: 0.8211 (mttt) REVERT: X 92 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: X 101 GLU cc_start: 0.7978 (mp0) cc_final: 0.7564 (mm-30) REVERT: X 142 LYS cc_start: 0.8035 (mttm) cc_final: 0.7751 (mptt) REVERT: D 36 GLN cc_start: 0.8345 (mt0) cc_final: 0.8052 (tt0) REVERT: D 78 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: D 93 ARG cc_start: 0.8168 (pmt170) cc_final: 0.7843 (pmt170) REVERT: D 110 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8301 (ttpt) REVERT: D 142 LYS cc_start: 0.7920 (mttm) cc_final: 0.7562 (mptt) REVERT: F 49 GLU cc_start: 0.8647 (tt0) cc_final: 0.8433 (tt0) REVERT: F 78 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: F 93 ARG cc_start: 0.8516 (pmt170) cc_final: 0.8313 (pmt170) REVERT: F 101 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: F 110 LYS cc_start: 0.8839 (tttm) cc_final: 0.8451 (ttpt) REVERT: F 118 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: R 78 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: R 110 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8423 (ttpt) REVERT: R 118 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: O 49 GLU cc_start: 0.8660 (tt0) cc_final: 0.8443 (tt0) REVERT: O 78 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: O 101 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: O 110 LYS cc_start: 0.8830 (tttm) cc_final: 0.8443 (ttpt) REVERT: O 118 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: C 78 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: C 101 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: C 110 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8418 (ttpt) REVERT: C 118 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: B 49 GLU cc_start: 0.8478 (tt0) cc_final: 0.8236 (tm-30) REVERT: B 142 LYS cc_start: 0.8076 (mttm) cc_final: 0.7821 (mptt) REVERT: W 87 MET cc_start: 0.7244 (pmt) cc_final: 0.6935 (mtp) REVERT: W 110 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8340 (ttpt) REVERT: W 125 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: K 49 GLU cc_start: 0.8706 (tt0) cc_final: 0.8431 (tt0) REVERT: K 78 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: K 82 LYS cc_start: 0.8194 (mttm) cc_final: 0.7928 (mtpt) REVERT: K 102 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: K 104 GLU cc_start: 0.7564 (tp30) cc_final: 0.7296 (mm-30) REVERT: K 142 LYS cc_start: 0.8141 (mttm) cc_final: 0.7938 (mptt) REVERT: N 103 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: N 123 LYS cc_start: 0.8615 (pttt) cc_final: 0.8224 (mttt) REVERT: H 110 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8322 (ttpt) REVERT: L 78 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: L 104 GLU cc_start: 0.7554 (tp30) cc_final: 0.7306 (mm-30) REVERT: L 142 LYS cc_start: 0.8204 (mttm) cc_final: 0.8003 (mptt) REVERT: M 49 GLU cc_start: 0.8586 (tt0) cc_final: 0.8363 (tt0) REVERT: M 82 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7864 (ptpt) REVERT: M 142 LYS cc_start: 0.8280 (mmtt) cc_final: 0.8047 (mptt) REVERT: M 145 ASN cc_start: 0.8371 (t0) cc_final: 0.8143 (m-40) REVERT: Q 92 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: Q 101 GLU cc_start: 0.8029 (mp0) cc_final: 0.7683 (mm-30) REVERT: Q 142 LYS cc_start: 0.8066 (mttm) cc_final: 0.7804 (mptt) REVERT: J 103 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: J 123 LYS cc_start: 0.8660 (pttt) cc_final: 0.8182 (mttt) REVERT: G 142 LYS cc_start: 0.8044 (mttm) cc_final: 0.7801 (mptt) REVERT: S 110 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8303 (ttpt) REVERT: V 78 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8300 (tm-30) outliers start: 112 outliers final: 16 residues processed: 717 average time/residue: 1.7280 time to fit residues: 1361.1735 Evaluate side-chains 586 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 541 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 139 SER Chi-restraints excluded: chain P residue 84 SER 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 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 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 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 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 N residue 103 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 Q residue 92 GLU Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain V residue 46 SER 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 178 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 53 HIS X 119 ASN D 119 ASN F 53 HIS O 53 HIS 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104715 restraints weight = 23532.690| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.20 r_work: 0.3013 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.7699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 21720 Z= 0.234 Angle : 0.771 9.988 29304 Z= 0.391 Chirality : 0.056 0.154 3480 Planarity : 0.005 0.041 3720 Dihedral : 4.831 15.962 2880 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.83 % Allowed : 20.42 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.10 (0.15), residues: 1392 loop : -0.79 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 59 HIS 0.007 0.002 HIS G 53 PHE 0.007 0.001 PHE L 124 TYR 0.009 0.002 TYR I 106 ARG 0.004 0.001 ARG D 93 Details of bonding type rmsd hydrogen bonds : bond 0.05423 ( 945) hydrogen bonds : angle 4.03202 ( 2331) covalent geometry : bond 0.00596 (21720) covalent geometry : angle 0.77101 (29304) *********************** 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 698 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 582 time to evaluate : 2.422 Fit side-chains REVERT: A 87 MET cc_start: 0.7578 (pmm) cc_final: 0.7353 (mmt) REVERT: A 101 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: A 123 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8442 (mttt) REVERT: A 142 LYS cc_start: 0.8292 (mttm) cc_final: 0.7983 (mptt) REVERT: P 87 MET cc_start: 0.7633 (pmm) cc_final: 0.7389 (mmt) REVERT: P 101 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: P 123 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8379 (mttp) REVERT: P 142 LYS cc_start: 0.8250 (mttm) cc_final: 0.7946 (mptt) REVERT: T 87 MET cc_start: 0.7572 (pmm) cc_final: 0.7358 (mmt) REVERT: T 101 GLU cc_start: 0.7936 (mp0) cc_final: 0.7247 (mm-30) REVERT: T 123 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8420 (mttt) REVERT: T 142 LYS cc_start: 0.8362 (mttm) cc_final: 0.8062 (mptt) REVERT: U 87 MET cc_start: 0.7637 (pmm) cc_final: 0.7388 (mmt) REVERT: U 101 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: U 123 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8375 (mttp) REVERT: U 142 LYS cc_start: 0.8275 (mttm) cc_final: 0.7972 (mptt) REVERT: E 102 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: E 104 GLU cc_start: 0.7711 (tp30) cc_final: 0.7396 (mm-30) REVERT: I 82 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7987 (ptpt) REVERT: I 101 GLU cc_start: 0.7924 (mp0) cc_final: 0.7276 (mm-30) REVERT: X 92 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: X 101 GLU cc_start: 0.7935 (mp0) cc_final: 0.7600 (mm-30) REVERT: X 142 LYS cc_start: 0.8296 (mttm) cc_final: 0.7978 (mptt) REVERT: D 36 GLN cc_start: 0.8314 (mt0) cc_final: 0.8099 (mt0) REVERT: D 78 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: D 103 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7640 (tm-30) REVERT: D 110 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8436 (tttm) REVERT: D 142 LYS cc_start: 0.8323 (mttm) cc_final: 0.7964 (mptt) REVERT: F 49 GLU cc_start: 0.8666 (tt0) cc_final: 0.8441 (tt0) REVERT: F 78 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: F 110 LYS cc_start: 0.8901 (tttm) cc_final: 0.8455 (ttpt) REVERT: F 118 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: F 142 LYS cc_start: 0.8302 (mptt) cc_final: 0.8099 (mptt) REVERT: R 78 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: R 110 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8438 (tttm) REVERT: R 118 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: O 49 GLU cc_start: 0.8658 (tt0) cc_final: 0.8438 (tt0) REVERT: O 78 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: O 110 LYS cc_start: 0.8895 (tttm) cc_final: 0.8461 (ttpt) REVERT: O 118 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: O 142 LYS cc_start: 0.8301 (mptt) cc_final: 0.8095 (mptt) REVERT: C 78 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: C 110 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8430 (tttm) REVERT: C 118 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: B 87 MET cc_start: 0.7478 (pmm) cc_final: 0.7132 (mmt) REVERT: B 101 GLU cc_start: 0.7966 (mp0) cc_final: 0.7591 (mm-30) REVERT: B 142 LYS cc_start: 0.8374 (mttm) cc_final: 0.8021 (mptt) REVERT: W 78 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: W 91 SER cc_start: 0.5391 (OUTLIER) cc_final: 0.5127 (t) REVERT: W 103 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7482 (tm-30) REVERT: W 110 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8422 (tttm) REVERT: W 125 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: K 102 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: K 104 GLU cc_start: 0.7687 (tp30) cc_final: 0.7377 (mm-30) REVERT: N 82 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7977 (ptpt) REVERT: N 101 GLU cc_start: 0.7931 (mp0) cc_final: 0.7278 (mm-30) REVERT: H 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: H 91 SER cc_start: 0.5458 (OUTLIER) cc_final: 0.5255 (t) REVERT: H 103 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7435 (tm-30) REVERT: H 110 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8304 (tttm) REVERT: L 78 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: L 102 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: L 104 GLU cc_start: 0.7663 (tp30) cc_final: 0.7370 (mm-30) REVERT: M 101 GLU cc_start: 0.7993 (mp0) cc_final: 0.7334 (mm-30) REVERT: Q 87 MET cc_start: 0.7400 (pmm) cc_final: 0.7043 (mmt) REVERT: Q 92 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: Q 101 GLU cc_start: 0.7918 (mp0) cc_final: 0.7629 (mm-30) REVERT: Q 142 LYS cc_start: 0.8336 (mttm) cc_final: 0.7992 (mptt) REVERT: J 78 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: J 101 GLU cc_start: 0.7959 (mp0) cc_final: 0.7259 (mm-30) REVERT: J 102 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: G 87 MET cc_start: 0.7448 (pmm) cc_final: 0.7134 (mmt) REVERT: G 101 GLU cc_start: 0.7964 (mp0) cc_final: 0.7605 (mm-30) REVERT: G 142 LYS cc_start: 0.8354 (mttm) cc_final: 0.8013 (mptt) REVERT: S 78 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: S 103 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7492 (tm-30) REVERT: S 110 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8324 (tttm) REVERT: V 78 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8313 (tm-30) REVERT: V 104 GLU cc_start: 0.7711 (tp30) cc_final: 0.7427 (mm-30) REVERT: V 123 LYS cc_start: 0.8956 (mttm) cc_final: 0.8725 (mttt) outliers start: 116 outliers final: 45 residues processed: 653 average time/residue: 1.6436 time to fit residues: 1182.5489 Evaluate side-chains 624 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 550 time to evaluate : 2.564 ------------------------------------------------------------------------------- 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 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 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 107 ARG Chi-restraints excluded: chain U residue 139 SER 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 X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER 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 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 145 ASN 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 102 GLU Chi-restraints excluded: chain N residue 139 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 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 102 GLU 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 115 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105949 restraints weight = 23671.887| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.26 r_work: 0.3066 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.7757 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= 0.145 Angle : 0.629 9.000 29304 Z= 0.316 Chirality : 0.053 0.149 3480 Planarity : 0.004 0.028 3720 Dihedral : 4.310 14.360 2880 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.12 % Allowed : 22.04 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.12 (0.15), residues: 1392 loop : -0.60 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE I 124 TYR 0.009 0.002 TYR J 106 ARG 0.002 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 945) hydrogen bonds : angle 3.80955 ( 2331) covalent geometry : bond 0.00352 (21720) covalent geometry : angle 0.62873 (29304) *********************** 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 674 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 575 time to evaluate : 2.699 Fit side-chains REVERT: A 78 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: A 87 MET cc_start: 0.7539 (pmm) cc_final: 0.7311 (mmt) REVERT: A 101 GLU cc_start: 0.7771 (mp0) cc_final: 0.7228 (mm-30) REVERT: A 123 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8361 (mttp) REVERT: A 142 LYS cc_start: 0.8222 (mttm) cc_final: 0.7868 (mptt) REVERT: P 78 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: P 87 MET cc_start: 0.7570 (pmm) cc_final: 0.7345 (mmt) REVERT: P 101 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7136 (mm-30) REVERT: P 103 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: P 123 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8321 (mttp) REVERT: P 142 LYS cc_start: 0.8171 (mttm) cc_final: 0.7831 (mptt) REVERT: T 49 GLU cc_start: 0.8602 (tt0) cc_final: 0.8402 (tt0) REVERT: T 78 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: T 87 MET cc_start: 0.7559 (pmm) cc_final: 0.7319 (mmt) REVERT: T 101 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7216 (mm-30) REVERT: T 123 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8351 (mttp) REVERT: T 142 LYS cc_start: 0.8249 (mttm) cc_final: 0.7920 (mptt) REVERT: U 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: U 87 MET cc_start: 0.7576 (pmm) cc_final: 0.7339 (mmt) REVERT: U 101 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: U 103 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: U 123 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8320 (mttp) REVERT: U 142 LYS cc_start: 0.8207 (mttm) cc_final: 0.7853 (mptt) REVERT: E 78 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: E 102 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: E 103 GLU cc_start: 0.7739 (tp30) cc_final: 0.7457 (tm-30) REVERT: I 101 GLU cc_start: 0.7876 (mp0) cc_final: 0.7264 (mm-30) REVERT: X 87 MET cc_start: 0.7409 (pmm) cc_final: 0.7039 (mmt) REVERT: X 92 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: X 101 GLU cc_start: 0.7927 (mp0) cc_final: 0.7579 (mm-30) REVERT: X 142 LYS cc_start: 0.8192 (mttm) cc_final: 0.7848 (mptt) REVERT: D 36 GLN cc_start: 0.8178 (mt0) cc_final: 0.7905 (tt0) REVERT: D 91 SER cc_start: 0.5316 (OUTLIER) cc_final: 0.5073 (t) REVERT: D 103 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7502 (tm-30) REVERT: D 110 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8376 (ttpt) REVERT: D 142 LYS cc_start: 0.8188 (mttm) cc_final: 0.7824 (mptt) REVERT: F 78 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: F 110 LYS cc_start: 0.8842 (tttm) cc_final: 0.8400 (ttpt) REVERT: F 118 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: R 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: R 110 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8419 (ttpt) REVERT: R 118 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: O 78 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: O 110 LYS cc_start: 0.8836 (tttm) cc_final: 0.8392 (ttpt) REVERT: O 118 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: C 78 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: C 101 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: C 110 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8351 (tttm) REVERT: C 118 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: B 87 MET cc_start: 0.7454 (pmm) cc_final: 0.7086 (mmt) REVERT: B 101 GLU cc_start: 0.7936 (mp0) cc_final: 0.7571 (mm-30) REVERT: B 142 LYS cc_start: 0.8248 (mttm) cc_final: 0.7871 (mptt) REVERT: W 78 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: W 91 SER cc_start: 0.5232 (OUTLIER) cc_final: 0.5013 (t) REVERT: W 103 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7307 (tm-30) REVERT: W 110 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8205 (tttm) REVERT: W 125 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: K 78 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: K 102 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: K 104 GLU cc_start: 0.7612 (tp30) cc_final: 0.7402 (mm-30) REVERT: N 101 GLU cc_start: 0.7864 (mp0) cc_final: 0.7241 (mm-30) REVERT: H 78 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: H 91 SER cc_start: 0.5371 (OUTLIER) cc_final: 0.5142 (t) REVERT: H 103 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7275 (tm-30) REVERT: H 110 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8155 (tttm) REVERT: L 49 GLU cc_start: 0.8573 (tt0) cc_final: 0.8322 (tt0) REVERT: L 78 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: L 104 GLU cc_start: 0.7619 (tp30) cc_final: 0.7396 (mm-30) REVERT: M 49 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: M 101 GLU cc_start: 0.7946 (mp0) cc_final: 0.7343 (mm-30) REVERT: M 102 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: Q 87 MET cc_start: 0.7385 (pmm) cc_final: 0.6998 (mmt) REVERT: Q 92 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: Q 101 GLU cc_start: 0.7890 (mp0) cc_final: 0.7591 (mm-30) REVERT: Q 142 LYS cc_start: 0.8205 (mttm) cc_final: 0.7842 (mptt) REVERT: J 78 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: J 101 GLU cc_start: 0.7962 (mp0) cc_final: 0.7295 (mm-30) REVERT: G 87 MET cc_start: 0.7400 (pmm) cc_final: 0.7068 (mmt) REVERT: G 101 GLU cc_start: 0.7933 (mp0) cc_final: 0.7577 (mm-30) REVERT: G 142 LYS cc_start: 0.8257 (mttm) cc_final: 0.7908 (mptt) REVERT: S 78 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: S 103 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7337 (tm-30) REVERT: S 110 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8175 (tttm) REVERT: V 78 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: V 104 GLU cc_start: 0.7649 (tp30) cc_final: 0.7435 (mm-30) outliers start: 99 outliers final: 31 residues processed: 647 average time/residue: 1.5362 time to fit residues: 1101.1085 Evaluate side-chains 631 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 562 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG 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 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 E residue 46 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 46 SER Chi-restraints excluded: chain D residue 91 SER 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 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 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 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 49 GLU Chi-restraints excluded: chain M residue 102 GLU 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 G residue 102 GLU Chi-restraints excluded: chain S residue 46 SER 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 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 118 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 54 optimal weight: 0.0170 chunk 172 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 134 optimal weight: 0.4980 chunk 256 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.1024 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.131021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104647 restraints weight = 23596.663| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.20 r_work: 0.3014 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.7774 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= 0.187 Angle : 0.688 9.419 29304 Z= 0.346 Chirality : 0.054 0.149 3480 Planarity : 0.004 0.036 3720 Dihedral : 4.514 14.484 2880 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.29 % Allowed : 23.29 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.07 (0.15), residues: 1392 loop : -0.62 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE J 124 TYR 0.010 0.002 TYR V 106 ARG 0.002 0.001 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 945) hydrogen bonds : angle 3.95038 ( 2331) covalent geometry : bond 0.00470 (21720) covalent geometry : angle 0.68769 (29304) *********************** 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: 103 poor density : 558 time to evaluate : 2.613 Fit side-chains REVERT: A 37 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8665 (mm) REVERT: A 78 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: A 87 MET cc_start: 0.7543 (pmm) cc_final: 0.7312 (mmt) REVERT: A 101 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: A 123 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8412 (mttp) REVERT: A 142 LYS cc_start: 0.8282 (mttm) cc_final: 0.7937 (mptt) REVERT: P 78 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: P 87 MET cc_start: 0.7565 (pmm) cc_final: 0.7340 (mmt) REVERT: P 101 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: P 103 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: P 123 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8379 (mttp) REVERT: P 142 LYS cc_start: 0.8276 (mttm) cc_final: 0.7986 (mptt) REVERT: T 78 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: T 87 MET cc_start: 0.7552 (pmm) cc_final: 0.7314 (mmt) REVERT: T 101 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: T 123 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8385 (mttp) REVERT: T 142 LYS cc_start: 0.8309 (mttm) cc_final: 0.7984 (mptt) REVERT: U 78 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: U 87 MET cc_start: 0.7583 (pmm) cc_final: 0.7342 (mmt) REVERT: U 101 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: U 103 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: U 123 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8388 (mttp) REVERT: U 142 LYS cc_start: 0.8295 (mttm) cc_final: 0.7996 (mptt) REVERT: E 78 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: E 102 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: I 101 GLU cc_start: 0.7957 (mp0) cc_final: 0.7487 (mm-30) REVERT: I 102 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: X 87 MET cc_start: 0.7496 (pmm) cc_final: 0.7168 (mmt) REVERT: X 92 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: X 101 GLU cc_start: 0.7918 (mp0) cc_final: 0.7613 (mm-30) REVERT: X 142 LYS cc_start: 0.8268 (mttm) cc_final: 0.7936 (mptt) REVERT: D 36 GLN cc_start: 0.8280 (mt0) cc_final: 0.8062 (tt0) REVERT: D 78 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: D 110 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8376 (tttm) REVERT: D 142 LYS cc_start: 0.8274 (mttm) cc_final: 0.7929 (mptt) REVERT: F 78 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: F 110 LYS cc_start: 0.8897 (tttm) cc_final: 0.8488 (ttpt) REVERT: F 118 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: R 78 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: R 110 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8442 (tttm) REVERT: R 118 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: O 78 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: O 110 LYS cc_start: 0.8870 (tttm) cc_final: 0.8480 (ttpt) REVERT: O 118 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: C 78 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: C 110 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8415 (tttm) REVERT: C 118 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 87 MET cc_start: 0.7498 (pmm) cc_final: 0.7202 (mmt) REVERT: B 101 GLU cc_start: 0.7930 (mp0) cc_final: 0.7604 (mm-30) REVERT: B 142 LYS cc_start: 0.8358 (mttm) cc_final: 0.8001 (mptt) REVERT: W 78 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: W 103 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7360 (tm-30) REVERT: W 110 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8400 (tttm) REVERT: W 125 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: K 78 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: K 102 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: K 104 GLU cc_start: 0.7657 (tp30) cc_final: 0.7408 (mm-30) REVERT: N 101 GLU cc_start: 0.7972 (mp0) cc_final: 0.7496 (mm-30) REVERT: N 102 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: H 78 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: H 102 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: H 103 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7410 (tm-30) REVERT: H 110 LYS cc_start: 0.9041 (ttmt) cc_final: 0.8359 (tttm) REVERT: L 49 GLU cc_start: 0.8601 (tt0) cc_final: 0.8353 (tt0) REVERT: L 78 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: L 104 GLU cc_start: 0.7636 (tp30) cc_final: 0.7407 (mm-30) REVERT: M 101 GLU cc_start: 0.7948 (mp0) cc_final: 0.7498 (mm-30) REVERT: M 102 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: Q 87 MET cc_start: 0.7452 (pmm) cc_final: 0.7098 (mmt) REVERT: Q 92 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: Q 101 GLU cc_start: 0.7896 (mp0) cc_final: 0.7629 (mm-30) REVERT: Q 142 LYS cc_start: 0.8346 (mttm) cc_final: 0.8000 (mptt) REVERT: J 78 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: J 101 GLU cc_start: 0.7960 (mp0) cc_final: 0.7415 (mm-30) REVERT: J 102 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: G 87 MET cc_start: 0.7487 (pmm) cc_final: 0.7198 (mmt) REVERT: G 101 GLU cc_start: 0.7935 (mp0) cc_final: 0.7616 (mm-30) REVERT: G 142 LYS cc_start: 0.8367 (mttm) cc_final: 0.8018 (mptt) REVERT: S 78 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: S 103 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7451 (tm-30) REVERT: S 110 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8355 (tttm) REVERT: V 78 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: V 104 GLU cc_start: 0.7721 (tp30) cc_final: 0.7498 (mm-30) outliers start: 103 outliers final: 46 residues processed: 627 average time/residue: 1.6115 time to fit residues: 1117.2673 Evaluate side-chains 636 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 550 time to evaluate : 2.418 ------------------------------------------------------------------------------- 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 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 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 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 46 SER Chi-restraints excluded: chain D residue 78 GLU 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 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 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 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 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 102 GLU 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 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 J residue 116 LYS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 67 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.131593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104712 restraints weight = 23297.690| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.19 r_work: 0.3037 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21720 Z= 0.127 Angle : 0.594 8.764 29304 Z= 0.298 Chirality : 0.052 0.146 3480 Planarity : 0.003 0.026 3720 Dihedral : 4.127 13.772 2880 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.33 % Allowed : 23.79 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.10 (0.15), residues: 1392 loop : -0.44 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 59 HIS 0.002 0.001 HIS T 53 PHE 0.005 0.001 PHE J 124 TYR 0.006 0.001 TYR J 106 ARG 0.001 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 945) hydrogen bonds : angle 3.80019 ( 2331) covalent geometry : bond 0.00301 (21720) covalent geometry : angle 0.59417 (29304) *********************** 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 682 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 578 time to evaluate : 2.479 Fit side-chains REVERT: A 37 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8636 (mm) REVERT: A 78 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: A 87 MET cc_start: 0.7533 (pmm) cc_final: 0.7305 (mmt) REVERT: A 101 GLU cc_start: 0.7781 (mp0) cc_final: 0.7348 (mm-30) REVERT: A 123 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8399 (mttp) REVERT: A 142 LYS cc_start: 0.8280 (mttm) cc_final: 0.7955 (mptt) REVERT: P 78 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: P 87 MET cc_start: 0.7557 (pmm) cc_final: 0.7323 (mmt) REVERT: P 101 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: P 103 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: P 123 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8376 (mttt) REVERT: P 142 LYS cc_start: 0.8205 (mttm) cc_final: 0.7890 (mptt) REVERT: T 78 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8218 (tm-30) REVERT: T 87 MET cc_start: 0.7537 (pmm) cc_final: 0.7307 (mmt) REVERT: T 101 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: T 123 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8395 (mttt) REVERT: T 142 LYS cc_start: 0.8283 (mttm) cc_final: 0.7983 (mptt) REVERT: U 78 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: U 87 MET cc_start: 0.7554 (pmm) cc_final: 0.7325 (mmt) REVERT: U 101 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: U 103 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: U 123 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8376 (mttt) REVERT: U 142 LYS cc_start: 0.8193 (mttm) cc_final: 0.7872 (mptt) REVERT: E 49 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: E 78 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: E 102 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: E 110 LYS cc_start: 0.8937 (tttm) cc_final: 0.8673 (tttm) REVERT: I 101 GLU cc_start: 0.7951 (mp0) cc_final: 0.7497 (mm-30) REVERT: I 102 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: X 87 MET cc_start: 0.7452 (pmm) cc_final: 0.7111 (mmt) REVERT: X 92 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: X 101 GLU cc_start: 0.7953 (mp0) cc_final: 0.7634 (mm-30) REVERT: X 142 LYS cc_start: 0.8217 (mttm) cc_final: 0.7895 (mptt) REVERT: D 36 GLN cc_start: 0.8219 (mt0) cc_final: 0.7973 (tt0) REVERT: D 78 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: D 110 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8422 (ttpt) REVERT: D 142 LYS cc_start: 0.8208 (mttm) cc_final: 0.7876 (mptt) REVERT: F 78 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: F 110 LYS cc_start: 0.8865 (tttm) cc_final: 0.8427 (ttpt) REVERT: F 118 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: R 78 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: R 110 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8503 (ttpt) REVERT: R 118 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: O 49 GLU cc_start: 0.8537 (tt0) cc_final: 0.8312 (tt0) REVERT: O 78 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: O 110 LYS cc_start: 0.8870 (tttm) cc_final: 0.8432 (ttpt) REVERT: O 118 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: C 78 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: C 101 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: C 110 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8477 (ttpt) REVERT: C 118 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: B 87 MET cc_start: 0.7486 (pmm) cc_final: 0.7153 (mmt) REVERT: B 101 GLU cc_start: 0.7930 (mp0) cc_final: 0.7607 (mm-30) REVERT: B 142 LYS cc_start: 0.8300 (mttm) cc_final: 0.7938 (mptt) REVERT: W 78 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: W 103 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7309 (tm-30) REVERT: W 110 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8395 (tttm) REVERT: W 125 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: K 49 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: K 78 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: K 102 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: K 104 GLU cc_start: 0.7624 (tp30) cc_final: 0.7404 (mm-30) REVERT: N 101 GLU cc_start: 0.7953 (mp0) cc_final: 0.7498 (mm-30) REVERT: N 102 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: H 78 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: H 103 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7332 (tm-30) REVERT: H 110 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8359 (tttm) REVERT: L 49 GLU cc_start: 0.8595 (tt0) cc_final: 0.8353 (tt0) REVERT: L 78 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: L 104 GLU cc_start: 0.7573 (tp30) cc_final: 0.7316 (mm-30) REVERT: L 110 LYS cc_start: 0.8959 (tttm) cc_final: 0.8695 (tttm) REVERT: M 49 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: M 101 GLU cc_start: 0.7946 (mp0) cc_final: 0.7509 (mm-30) REVERT: M 102 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: Q 87 MET cc_start: 0.7426 (pmm) cc_final: 0.7044 (mmt) REVERT: Q 101 GLU cc_start: 0.7885 (mp0) cc_final: 0.7657 (mm-30) REVERT: Q 142 LYS cc_start: 0.8270 (mttm) cc_final: 0.7930 (mptt) REVERT: J 78 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: J 101 GLU cc_start: 0.7949 (mp0) cc_final: 0.7428 (mm-30) REVERT: J 102 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: G 87 MET cc_start: 0.7431 (pmm) cc_final: 0.7108 (mmt) REVERT: G 101 GLU cc_start: 0.7905 (mp0) cc_final: 0.7625 (mm-30) REVERT: G 142 LYS cc_start: 0.8293 (mttm) cc_final: 0.7947 (mptt) REVERT: S 78 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: S 103 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7402 (tm-30) REVERT: S 110 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8361 (tttm) REVERT: V 78 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: V 104 GLU cc_start: 0.7656 (tp30) cc_final: 0.7407 (mm-30) REVERT: V 110 LYS cc_start: 0.8954 (tttm) cc_final: 0.8693 (tttm) outliers start: 104 outliers final: 50 residues processed: 645 average time/residue: 1.5879 time to fit residues: 1133.5517 Evaluate side-chains 669 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 578 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 102 GLU Chi-restraints excluded: chain A residue 107 ARG 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 P residue 121 SER 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 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 121 SER 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 E residue 145 ASN 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 D residue 78 GLU Chi-restraints excluded: chain D residue 121 SER 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 B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER 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 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 N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 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 139 SER Chi-restraints excluded: chain Q residue 102 GLU 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 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 46 SER Chi-restraints excluded: chain S residue 78 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 181 optimal weight: 0.1980 chunk 221 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.130770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104154 restraints weight = 23441.283| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.22 r_work: 0.3047 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.004 0.026 21720 Z= 0.173 Angle : 0.663 9.148 29304 Z= 0.333 Chirality : 0.054 0.147 3480 Planarity : 0.004 0.033 3720 Dihedral : 4.360 13.625 2880 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.71 % Allowed : 24.00 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.03 (0.15), residues: 1392 loop : -0.48 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE J 124 TYR 0.009 0.002 TYR P 106 ARG 0.002 0.000 ARG H 93 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 945) hydrogen bonds : angle 3.91325 ( 2331) covalent geometry : bond 0.00433 (21720) covalent geometry : angle 0.66275 (29304) *********************** 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 665 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 552 time to evaluate : 2.663 Fit side-chains REVERT: A 37 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8622 (mm) REVERT: A 78 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: A 87 MET cc_start: 0.7517 (pmm) cc_final: 0.7299 (mmt) REVERT: A 101 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: A 123 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8373 (mttp) REVERT: A 142 LYS cc_start: 0.8240 (mttm) cc_final: 0.7893 (mptt) REVERT: P 78 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: P 87 MET cc_start: 0.7531 (pmm) cc_final: 0.7316 (mmt) REVERT: P 101 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: P 103 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: P 123 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8326 (mttt) REVERT: P 142 LYS cc_start: 0.8215 (mttm) cc_final: 0.7870 (mptt) REVERT: T 78 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: T 87 MET cc_start: 0.7549 (pmm) cc_final: 0.7318 (mmt) REVERT: T 101 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: T 123 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8337 (mttp) REVERT: T 142 LYS cc_start: 0.8255 (mttm) cc_final: 0.7927 (mptt) REVERT: U 37 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8634 (mm) REVERT: U 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: U 87 MET cc_start: 0.7550 (pmm) cc_final: 0.7306 (mmt) REVERT: U 101 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: U 103 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: U 123 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8322 (mttt) REVERT: U 142 LYS cc_start: 0.8221 (mttm) cc_final: 0.7870 (mptt) REVERT: E 49 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: E 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: E 102 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: I 101 GLU cc_start: 0.7930 (mp0) cc_final: 0.7500 (mm-30) REVERT: I 102 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: X 87 MET cc_start: 0.7440 (pmm) cc_final: 0.7151 (mmt) REVERT: X 92 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: X 101 GLU cc_start: 0.7933 (mp0) cc_final: 0.7606 (mm-30) REVERT: X 142 LYS cc_start: 0.8225 (mttm) cc_final: 0.7879 (mptt) REVERT: D 36 GLN cc_start: 0.8234 (mt0) cc_final: 0.7987 (tt0) REVERT: D 78 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: D 110 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8325 (tttm) REVERT: D 142 LYS cc_start: 0.8195 (mttm) cc_final: 0.7844 (mptt) REVERT: F 78 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8218 (tm-30) REVERT: F 110 LYS cc_start: 0.8859 (tttm) cc_final: 0.8387 (ttpt) REVERT: F 118 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: R 78 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: R 110 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8380 (tttm) REVERT: R 118 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: O 49 GLU cc_start: 0.8534 (tt0) cc_final: 0.8290 (tt0) REVERT: O 78 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: O 110 LYS cc_start: 0.8851 (tttm) cc_final: 0.8391 (ttpt) REVERT: O 118 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: C 78 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: C 110 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8363 (tttm) REVERT: C 118 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: B 87 MET cc_start: 0.7475 (pmm) cc_final: 0.7161 (mmt) REVERT: B 101 GLU cc_start: 0.7940 (mp0) cc_final: 0.7583 (mm-30) REVERT: B 142 LYS cc_start: 0.8346 (mttm) cc_final: 0.7973 (mptt) REVERT: W 78 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: W 102 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: W 103 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7310 (tm-30) REVERT: W 110 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8316 (tttm) REVERT: W 125 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: K 49 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: K 78 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: K 102 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: K 104 GLU cc_start: 0.7620 (tp30) cc_final: 0.7379 (mm-30) REVERT: N 101 GLU cc_start: 0.7924 (mp0) cc_final: 0.7497 (mm-30) REVERT: N 102 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: H 78 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: H 102 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: H 103 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7343 (tm-30) REVERT: H 110 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8295 (tttm) REVERT: L 49 GLU cc_start: 0.8576 (tt0) cc_final: 0.8317 (tt0) REVERT: L 78 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: L 104 GLU cc_start: 0.7576 (tp30) cc_final: 0.7346 (mm-30) REVERT: M 49 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: M 101 GLU cc_start: 0.7927 (mp0) cc_final: 0.7471 (mm-30) REVERT: M 102 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: Q 87 MET cc_start: 0.7449 (pmm) cc_final: 0.7107 (mmt) REVERT: Q 101 GLU cc_start: 0.7892 (mp0) cc_final: 0.7629 (mm-30) REVERT: Q 142 LYS cc_start: 0.8273 (mttm) cc_final: 0.7905 (mptt) REVERT: J 78 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: J 101 GLU cc_start: 0.7897 (mp0) cc_final: 0.7459 (mm-30) REVERT: J 102 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: G 87 MET cc_start: 0.7455 (pmm) cc_final: 0.7146 (mmt) REVERT: G 101 GLU cc_start: 0.7940 (mp0) cc_final: 0.7601 (mm-30) REVERT: G 142 LYS cc_start: 0.8305 (mttm) cc_final: 0.7939 (mptt) REVERT: S 78 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: S 102 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: S 103 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7385 (tm-30) REVERT: S 110 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8288 (tttm) REVERT: V 78 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: V 104 GLU cc_start: 0.7607 (tp30) cc_final: 0.7350 (mm-30) outliers start: 113 outliers final: 55 residues processed: 627 average time/residue: 1.5630 time to fit residues: 1084.6823 Evaluate side-chains 653 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 553 time to evaluate : 2.559 ------------------------------------------------------------------------------- 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 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 121 SER 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 37 ILE 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 121 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 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 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 D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 121 SER 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 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 102 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 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 102 GLU 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 139 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 121 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.132611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105806 restraints weight = 23623.823| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.25 r_work: 0.3066 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 21720 Z= 0.133 Angle : 0.605 8.824 29304 Z= 0.303 Chirality : 0.053 0.146 3480 Planarity : 0.003 0.027 3720 Dihedral : 4.142 13.347 2880 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.46 % Allowed : 24.42 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.06 (0.15), residues: 1392 loop : -0.37 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 59 HIS 0.002 0.001 HIS T 53 PHE 0.005 0.001 PHE J 124 TYR 0.005 0.001 TYR J 106 ARG 0.001 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 945) hydrogen bonds : angle 3.83309 ( 2331) covalent geometry : bond 0.00318 (21720) covalent geometry : angle 0.60500 (29304) *********************** 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 678 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 571 time to evaluate : 2.571 Fit side-chains REVERT: A 37 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8603 (mm) REVERT: A 78 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: A 87 MET cc_start: 0.7520 (pmm) cc_final: 0.7279 (mmt) REVERT: A 101 GLU cc_start: 0.7801 (mp0) cc_final: 0.7408 (mm-30) REVERT: A 123 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8366 (mttp) REVERT: A 142 LYS cc_start: 0.8204 (mttm) cc_final: 0.7875 (mptt) REVERT: P 78 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: P 87 MET cc_start: 0.7545 (pmm) cc_final: 0.7304 (mmt) REVERT: P 101 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: P 103 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: P 123 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8344 (mttt) REVERT: P 142 LYS cc_start: 0.8180 (mttm) cc_final: 0.7851 (mptt) REVERT: T 49 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: T 78 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: T 87 MET cc_start: 0.7533 (pmm) cc_final: 0.7282 (mmt) REVERT: T 101 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: T 123 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8366 (mttt) REVERT: T 142 LYS cc_start: 0.8189 (mttm) cc_final: 0.7883 (mptt) REVERT: U 37 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8609 (mm) REVERT: U 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: U 87 MET cc_start: 0.7558 (pmm) cc_final: 0.7294 (mmt) REVERT: U 101 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: U 103 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: U 123 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8351 (mttt) REVERT: U 142 LYS cc_start: 0.8181 (mttm) cc_final: 0.7852 (mptt) REVERT: E 49 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: E 78 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: E 102 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: E 110 LYS cc_start: 0.8905 (tttm) cc_final: 0.8634 (tttm) REVERT: I 101 GLU cc_start: 0.7924 (mp0) cc_final: 0.7510 (mm-30) REVERT: I 102 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: X 87 MET cc_start: 0.7408 (pmm) cc_final: 0.7108 (mmt) REVERT: X 92 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: X 101 GLU cc_start: 0.7940 (mp0) cc_final: 0.7594 (mm-30) REVERT: X 142 LYS cc_start: 0.8164 (mttm) cc_final: 0.7832 (mptt) REVERT: D 36 GLN cc_start: 0.8199 (mt0) cc_final: 0.7946 (tt0) REVERT: D 78 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: D 110 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8348 (ttpt) REVERT: D 142 LYS cc_start: 0.8162 (mttm) cc_final: 0.7813 (mptt) REVERT: F 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8218 (tm-30) REVERT: F 110 LYS cc_start: 0.8844 (tttm) cc_final: 0.8390 (ttpt) REVERT: F 118 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: R 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: R 110 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8401 (ttpt) REVERT: R 118 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: O 49 GLU cc_start: 0.8540 (tt0) cc_final: 0.8311 (tt0) REVERT: O 78 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: O 110 LYS cc_start: 0.8836 (tttm) cc_final: 0.8381 (ttpt) REVERT: O 118 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 78 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: C 101 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: C 110 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8393 (ttpt) REVERT: C 118 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: B 87 MET cc_start: 0.7453 (pmm) cc_final: 0.7113 (mmt) REVERT: B 101 GLU cc_start: 0.7935 (mp0) cc_final: 0.7572 (mm-30) REVERT: B 142 LYS cc_start: 0.8283 (mttm) cc_final: 0.7920 (mptt) REVERT: W 78 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: W 103 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7252 (tm-30) REVERT: W 110 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8317 (tttm) REVERT: W 125 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: K 49 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: K 78 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: K 102 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: K 104 GLU cc_start: 0.7600 (tp30) cc_final: 0.7362 (mm-30) REVERT: N 101 GLU cc_start: 0.7916 (mp0) cc_final: 0.7502 (mm-30) REVERT: N 102 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: H 78 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: H 102 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: H 110 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8279 (tttm) REVERT: L 49 GLU cc_start: 0.8581 (tt0) cc_final: 0.8332 (tt0) REVERT: L 78 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: L 104 GLU cc_start: 0.7552 (tp30) cc_final: 0.7326 (mm-30) REVERT: L 110 LYS cc_start: 0.8913 (tttm) cc_final: 0.8641 (tttm) REVERT: M 49 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: M 101 GLU cc_start: 0.7908 (mp0) cc_final: 0.7457 (mm-30) REVERT: M 102 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: Q 87 MET cc_start: 0.7432 (pmm) cc_final: 0.7053 (mmt) REVERT: Q 101 GLU cc_start: 0.7894 (mp0) cc_final: 0.7612 (mm-30) REVERT: Q 142 LYS cc_start: 0.8224 (mttm) cc_final: 0.7870 (mptt) REVERT: J 78 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: J 101 GLU cc_start: 0.7890 (mp0) cc_final: 0.7448 (mm-30) REVERT: J 102 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: G 87 MET cc_start: 0.7435 (pmm) cc_final: 0.7102 (mmt) REVERT: G 101 GLU cc_start: 0.7934 (mp0) cc_final: 0.7599 (mm-30) REVERT: G 142 LYS cc_start: 0.8234 (mttm) cc_final: 0.7886 (mptt) REVERT: S 78 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: S 102 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: S 103 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7357 (tm-30) REVERT: S 110 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8288 (tttm) REVERT: V 78 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: V 104 GLU cc_start: 0.7571 (tp30) cc_final: 0.7310 (mm-30) REVERT: V 110 LYS cc_start: 0.8912 (tttm) cc_final: 0.8644 (tttm) outliers start: 107 outliers final: 62 residues processed: 643 average time/residue: 1.5835 time to fit residues: 1130.6232 Evaluate side-chains 682 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 575 time to evaluate : 2.460 ------------------------------------------------------------------------------- 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 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 121 SER 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 P residue 121 SER Chi-restraints excluded: chain T residue 49 GLU 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 37 ILE 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 121 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 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 E residue 145 ASN 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 121 SER Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 40 LYS 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 40 LYS 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 40 LYS 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 40 LYS 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 121 SER Chi-restraints excluded: chain B residue 139 SER 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 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 121 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 78 GLU 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 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 139 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 121 SER 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 116 LYS Chi-restraints excluded: chain J residue 121 SER 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 40 LYS Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 192 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 256 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 126 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.136088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109916 restraints weight = 23215.648| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.15 r_work: 0.3103 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 21720 Z= 0.081 Angle : 0.507 7.809 29304 Z= 0.254 Chirality : 0.051 0.139 3480 Planarity : 0.003 0.022 3720 Dihedral : 3.590 12.219 2880 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.58 % Allowed : 25.29 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.16 (0.15), residues: 1392 loop : -0.06 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP V 59 HIS 0.002 0.000 HIS T 53 PHE 0.004 0.000 PHE J 124 TYR 0.009 0.001 TYR J 106 ARG 0.001 0.000 ARG T 107 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 945) hydrogen bonds : angle 3.67919 ( 2331) covalent geometry : bond 0.00175 (21720) covalent geometry : angle 0.50719 (29304) *********************** 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 663 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 577 time to evaluate : 2.724 Fit side-chains REVERT: A 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: A 87 MET cc_start: 0.7454 (pmm) cc_final: 0.7147 (mmt) REVERT: A 101 GLU cc_start: 0.7791 (mp0) cc_final: 0.7388 (mm-30) REVERT: A 123 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8385 (mttt) REVERT: A 142 LYS cc_start: 0.8032 (mttm) cc_final: 0.7737 (mptt) REVERT: P 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: P 87 MET cc_start: 0.7481 (pmm) cc_final: 0.7202 (mmt) REVERT: P 101 GLU cc_start: 0.7695 (mp0) cc_final: 0.7213 (mm-30) REVERT: P 103 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: P 123 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8348 (mttt) REVERT: P 142 LYS cc_start: 0.8007 (mttm) cc_final: 0.7703 (mptt) REVERT: T 87 MET cc_start: 0.7476 (pmm) cc_final: 0.7161 (mmt) REVERT: T 101 GLU cc_start: 0.7804 (mp0) cc_final: 0.7319 (mm-30) REVERT: T 123 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8317 (mttt) REVERT: T 142 LYS cc_start: 0.8073 (mttm) cc_final: 0.7813 (mptt) REVERT: U 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: U 87 MET cc_start: 0.7498 (pmm) cc_final: 0.7197 (mmt) REVERT: U 101 GLU cc_start: 0.7688 (mp0) cc_final: 0.7208 (mm-30) REVERT: U 103 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: U 123 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8350 (mttt) REVERT: U 142 LYS cc_start: 0.7995 (mttm) cc_final: 0.7687 (mptt) REVERT: E 78 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: E 110 LYS cc_start: 0.8872 (tttm) cc_final: 0.8606 (tttm) REVERT: I 101 GLU cc_start: 0.7885 (mp0) cc_final: 0.7466 (mm-30) REVERT: X 101 GLU cc_start: 0.7857 (mp0) cc_final: 0.7513 (mm-30) REVERT: X 142 LYS cc_start: 0.7989 (mttm) cc_final: 0.7713 (mptt) REVERT: D 78 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: D 110 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8077 (tttm) REVERT: D 142 LYS cc_start: 0.8019 (mttm) cc_final: 0.7718 (mptt) REVERT: F 101 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: F 110 LYS cc_start: 0.8799 (tttm) cc_final: 0.8385 (ttpt) REVERT: F 118 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: F 142 LYS cc_start: 0.8116 (mptt) cc_final: 0.7906 (mptt) REVERT: R 110 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8337 (ttpt) REVERT: R 118 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: O 101 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: O 110 LYS cc_start: 0.8785 (tttm) cc_final: 0.8398 (ttpt) REVERT: O 118 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: C 101 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: C 110 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8366 (ttpt) REVERT: C 118 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: B 87 MET cc_start: 0.7372 (pmm) cc_final: 0.6955 (mmt) REVERT: B 101 GLU cc_start: 0.7888 (mp0) cc_final: 0.7548 (mm-30) REVERT: B 142 LYS cc_start: 0.8097 (mttm) cc_final: 0.7835 (mptt) REVERT: W 78 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: W 103 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7182 (tm-30) REVERT: W 110 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8118 (tttm) REVERT: W 125 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: K 78 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: N 101 GLU cc_start: 0.7893 (mp0) cc_final: 0.7457 (mm-30) REVERT: N 142 LYS cc_start: 0.8062 (mptt) cc_final: 0.7732 (mptt) REVERT: H 78 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: H 110 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8105 (tttm) REVERT: L 49 GLU cc_start: 0.8538 (tt0) cc_final: 0.8278 (tt0) REVERT: L 110 LYS cc_start: 0.8881 (tttm) cc_final: 0.8616 (tttm) REVERT: M 101 GLU cc_start: 0.7907 (mp0) cc_final: 0.7434 (mm-30) REVERT: Q 87 MET cc_start: 0.7321 (pmm) cc_final: 0.6883 (mmt) REVERT: Q 101 GLU cc_start: 0.7828 (mp0) cc_final: 0.7562 (mm-30) REVERT: Q 142 LYS cc_start: 0.8044 (mttm) cc_final: 0.7785 (mptt) REVERT: J 101 GLU cc_start: 0.7875 (mp0) cc_final: 0.7399 (mm-30) REVERT: J 142 LYS cc_start: 0.8080 (mptt) cc_final: 0.7759 (mptt) REVERT: G 87 MET cc_start: 0.7315 (pmm) cc_final: 0.6918 (mmt) REVERT: G 101 GLU cc_start: 0.7862 (mp0) cc_final: 0.7559 (mm-30) REVERT: G 142 LYS cc_start: 0.8056 (mttm) cc_final: 0.7802 (mptt) REVERT: S 78 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: S 103 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7228 (tm-30) REVERT: S 110 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8110 (tttm) REVERT: V 78 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: V 110 LYS cc_start: 0.8880 (tttm) cc_final: 0.8613 (tttm) outliers start: 86 outliers final: 44 residues processed: 630 average time/residue: 1.4716 time to fit residues: 1031.1372 Evaluate side-chains 630 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 564 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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 78 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 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 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 E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN 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 78 GLU Chi-restraints excluded: chain D 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 139 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 78 GLU Chi-restraints excluded: chain K 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 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 116 LYS 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 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 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 30 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 255 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.132157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104961 restraints weight = 22977.189| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.21 r_work: 0.3023 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.003 0.020 21720 Z= 0.141 Angle : 0.616 8.694 29304 Z= 0.308 Chirality : 0.053 0.145 3480 Planarity : 0.003 0.031 3720 Dihedral : 4.012 13.004 2880 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.79 % Allowed : 27.00 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.11 (0.15), residues: 1392 loop : -0.21 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE I 124 TYR 0.005 0.001 TYR V 96 ARG 0.001 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 945) hydrogen bonds : angle 3.83144 ( 2331) covalent geometry : bond 0.00340 (21720) covalent geometry : angle 0.61600 (29304) ********************** 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 631 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 564 time to evaluate : 2.769 Fit side-chains REVERT: A 78 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: A 87 MET cc_start: 0.7500 (pmm) cc_final: 0.7227 (mmt) REVERT: A 101 GLU cc_start: 0.7776 (mp0) cc_final: 0.7381 (mm-30) REVERT: A 123 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8362 (mttt) REVERT: A 142 LYS cc_start: 0.8191 (mttm) cc_final: 0.7869 (mptt) REVERT: P 78 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: P 87 MET cc_start: 0.7469 (pmm) cc_final: 0.7219 (mmt) REVERT: P 101 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: P 103 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: P 123 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8343 (mttt) REVERT: P 142 LYS cc_start: 0.8118 (mttm) cc_final: 0.7793 (mptt) REVERT: T 78 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: T 87 MET cc_start: 0.7517 (pmm) cc_final: 0.7228 (mmt) REVERT: T 101 GLU cc_start: 0.7816 (mp0) cc_final: 0.7354 (mm-30) REVERT: T 123 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8349 (mttt) REVERT: T 142 LYS cc_start: 0.8183 (mttm) cc_final: 0.7884 (mptt) REVERT: U 78 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: U 87 MET cc_start: 0.7473 (pmm) cc_final: 0.7211 (mmt) REVERT: U 101 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: U 103 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: U 123 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8333 (mttt) REVERT: U 142 LYS cc_start: 0.8124 (mttm) cc_final: 0.7789 (mptt) REVERT: E 78 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: E 110 LYS cc_start: 0.8843 (tttm) cc_final: 0.8567 (tttm) REVERT: I 101 GLU cc_start: 0.7879 (mp0) cc_final: 0.7464 (mm-30) REVERT: X 87 MET cc_start: 0.7365 (pmm) cc_final: 0.6979 (mmt) REVERT: X 101 GLU cc_start: 0.7908 (mp0) cc_final: 0.7570 (mm-30) REVERT: X 142 LYS cc_start: 0.8155 (mttm) cc_final: 0.7856 (mptt) REVERT: D 78 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: D 110 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8109 (tttm) REVERT: D 142 LYS cc_start: 0.8151 (mttm) cc_final: 0.7802 (mptt) REVERT: F 78 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: F 110 LYS cc_start: 0.8810 (tttm) cc_final: 0.8235 (tttm) REVERT: F 118 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: R 78 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: R 110 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8375 (ttpt) REVERT: R 118 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: O 78 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: O 110 LYS cc_start: 0.8814 (tttm) cc_final: 0.8256 (tttm) REVERT: O 118 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 78 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: C 101 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: C 110 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8366 (ttpt) REVERT: C 118 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: B 87 MET cc_start: 0.7386 (pmm) cc_final: 0.7016 (mmt) REVERT: B 101 GLU cc_start: 0.7909 (mp0) cc_final: 0.7550 (mm-30) REVERT: B 142 LYS cc_start: 0.8246 (mttm) cc_final: 0.7893 (mptt) REVERT: W 78 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: W 102 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: W 103 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7266 (tm-30) REVERT: W 110 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8118 (tttm) REVERT: W 125 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: K 78 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: N 101 GLU cc_start: 0.7882 (mp0) cc_final: 0.7472 (mm-30) REVERT: H 78 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: H 110 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8085 (tttm) REVERT: L 49 GLU cc_start: 0.8540 (tt0) cc_final: 0.8262 (tt0) REVERT: L 110 LYS cc_start: 0.8894 (tttm) cc_final: 0.8621 (tttm) REVERT: M 101 GLU cc_start: 0.7884 (mp0) cc_final: 0.7426 (mm-30) REVERT: Q 87 MET cc_start: 0.7315 (pmm) cc_final: 0.6918 (mmt) REVERT: Q 101 GLU cc_start: 0.7799 (mp0) cc_final: 0.7556 (mm-30) REVERT: Q 142 LYS cc_start: 0.8202 (mttm) cc_final: 0.7858 (mptt) REVERT: J 101 GLU cc_start: 0.7854 (mp0) cc_final: 0.7399 (mm-30) REVERT: G 87 MET cc_start: 0.7335 (pmm) cc_final: 0.6977 (mmt) REVERT: G 101 GLU cc_start: 0.7879 (mp0) cc_final: 0.7560 (mm-30) REVERT: G 142 LYS cc_start: 0.8207 (mttm) cc_final: 0.7858 (mptt) REVERT: S 78 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: S 103 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7321 (tm-30) REVERT: S 110 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8090 (tttm) REVERT: V 78 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: V 110 LYS cc_start: 0.8890 (tttm) cc_final: 0.8615 (tttm) outliers start: 67 outliers final: 42 residues processed: 611 average time/residue: 1.6039 time to fit residues: 1083.8575 Evaluate side-chains 630 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 560 time to evaluate : 2.488 ------------------------------------------------------------------------------- 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 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 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 E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 46 SER 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 40 LYS 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 40 LYS 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 W residue 145 ASN Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain H 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 Q residue 145 ASN 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 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 69 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 209 optimal weight: 0.0670 chunk 148 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 243 optimal weight: 0.6980 overall best weight: 2.3524 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.131406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104376 restraints weight = 22819.652| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.18 r_work: 0.3014 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.7875 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= 0.152 Angle : 0.640 9.192 29304 Z= 0.320 Chirality : 0.053 0.146 3480 Planarity : 0.004 0.030 3720 Dihedral : 4.156 13.239 2880 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.67 % Allowed : 27.62 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.07 (0.15), residues: 1392 loop : -0.28 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE I 124 TYR 0.011 0.002 TYR U 106 ARG 0.001 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 945) hydrogen bonds : angle 3.87050 ( 2331) covalent geometry : bond 0.00371 (21720) covalent geometry : angle 0.64015 (29304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23932.04 seconds wall clock time: 409 minutes 49.43 seconds (24589.43 seconds total)