Starting phenix.real_space_refine on Wed Jun 18 11:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp9_37713/06_2025/8wp9_37713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp9_37713/06_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_37713/06_2025/8wp9_37713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp9_37713/06_2025/8wp9_37713.map" model { file = "/net/cci-nas-00/data/ceres_data/8wp9_37713/06_2025/8wp9_37713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp9_37713/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.22, per 1000 atoms: 0.29 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: 4.97 Conformation dependent library (CDL) restraints added in 2.7 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: 3.87 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: 8.85 Time building geometry restraints manager: 5.92 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: 3.400 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: 1.040 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 45.300 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.000 ------------------------------------------------------------------------------- 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 : 2.856 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: 1.7134 time to fit residues: 1554.8904 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 : 2.388 ------------------------------------------------------------------------------- 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 = 0.135690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109432 restraints weight = 23730.694| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.24 r_work: 0.3085 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.64 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 : 2.604 Fit side-chains REVERT: A 87 MET cc_start: 0.7592 (pmm) cc_final: 0.7158 (mmp) REVERT: A 93 ARG cc_start: 0.8543 (pmt170) cc_final: 0.8209 (pmt170) REVERT: A 101 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: A 102 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: A 123 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8359 (mttp) REVERT: A 142 LYS cc_start: 0.8126 (mttm) cc_final: 0.7776 (mptt) REVERT: P 87 MET cc_start: 0.7578 (pmm) cc_final: 0.7214 (mmp) REVERT: P 123 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8353 (mttt) REVERT: P 142 LYS cc_start: 0.8127 (mttm) cc_final: 0.7779 (mptt) REVERT: T 87 MET cc_start: 0.7584 (pmm) cc_final: 0.7154 (mmp) REVERT: T 101 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: T 123 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8316 (mttt) REVERT: T 142 LYS cc_start: 0.8081 (mttm) cc_final: 0.7774 (mptt) REVERT: U 87 MET cc_start: 0.7581 (pmm) cc_final: 0.7214 (mmp) REVERT: U 123 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8356 (mttt) REVERT: U 142 LYS cc_start: 0.8069 (mttm) cc_final: 0.7733 (mptt) REVERT: E 49 GLU cc_start: 0.8690 (tt0) cc_final: 0.8415 (tt0) REVERT: E 78 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: E 82 LYS cc_start: 0.8187 (mttm) cc_final: 0.7919 (mtpt) REVERT: E 102 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: E 104 GLU cc_start: 0.7572 (tp30) cc_final: 0.7304 (mm-30) REVERT: I 103 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: I 123 LYS cc_start: 0.8606 (pttt) cc_final: 0.8212 (mttt) REVERT: X 92 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: X 101 GLU cc_start: 0.7980 (mp0) cc_final: 0.7566 (mm-30) REVERT: X 142 LYS cc_start: 0.8032 (mttm) cc_final: 0.7748 (mptt) REVERT: D 36 GLN cc_start: 0.8346 (mt0) cc_final: 0.8054 (tt0) REVERT: D 78 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: D 93 ARG cc_start: 0.8167 (pmt170) cc_final: 0.7839 (pmt170) REVERT: D 110 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8303 (ttpt) REVERT: D 142 LYS cc_start: 0.7917 (mttm) cc_final: 0.7559 (mptt) REVERT: F 49 GLU cc_start: 0.8645 (tt0) cc_final: 0.8429 (tt0) REVERT: F 78 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: F 93 ARG cc_start: 0.8515 (pmt170) cc_final: 0.8311 (pmt170) REVERT: F 101 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: F 110 LYS cc_start: 0.8837 (tttm) cc_final: 0.8451 (ttpt) REVERT: F 118 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: R 78 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: R 110 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8423 (ttpt) REVERT: R 118 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: O 49 GLU cc_start: 0.8657 (tt0) cc_final: 0.8438 (tt0) REVERT: O 78 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: O 101 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: O 110 LYS cc_start: 0.8830 (tttm) cc_final: 0.8443 (ttpt) REVERT: O 118 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: C 78 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: C 101 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: C 110 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8418 (ttpt) REVERT: C 118 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: B 49 GLU cc_start: 0.8477 (tt0) cc_final: 0.8234 (tm-30) REVERT: B 142 LYS cc_start: 0.8072 (mttm) cc_final: 0.7816 (mptt) REVERT: W 87 MET cc_start: 0.7243 (pmt) cc_final: 0.6932 (mtp) REVERT: W 110 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8341 (ttpt) REVERT: W 125 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: K 49 GLU cc_start: 0.8705 (tt0) cc_final: 0.8429 (tt0) REVERT: K 78 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: K 82 LYS cc_start: 0.8195 (mttm) cc_final: 0.7929 (mtpt) REVERT: K 102 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: K 104 GLU cc_start: 0.7566 (tp30) cc_final: 0.7298 (mm-30) REVERT: K 142 LYS cc_start: 0.8138 (mttm) cc_final: 0.7935 (mptt) REVERT: N 103 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: N 123 LYS cc_start: 0.8616 (pttt) cc_final: 0.8225 (mttt) REVERT: H 110 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8322 (ttpt) REVERT: L 78 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: L 104 GLU cc_start: 0.7556 (tp30) cc_final: 0.7309 (mm-30) REVERT: L 142 LYS cc_start: 0.8200 (mttm) cc_final: 0.7997 (mptt) REVERT: M 49 GLU cc_start: 0.8586 (tt0) cc_final: 0.8365 (tt0) REVERT: M 82 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7863 (ptpt) REVERT: M 142 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8043 (mptt) REVERT: M 145 ASN cc_start: 0.8372 (t0) cc_final: 0.8144 (m-40) REVERT: Q 92 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: Q 101 GLU cc_start: 0.8031 (mp0) cc_final: 0.7683 (mm-30) REVERT: Q 142 LYS cc_start: 0.8064 (mttm) cc_final: 0.7801 (mptt) REVERT: J 103 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8043 (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: 0.7799 (mptt) REVERT: S 110 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8305 (ttpt) REVERT: V 78 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8301 (tm-30) outliers start: 112 outliers final: 16 residues processed: 717 average time/residue: 1.7834 time to fit residues: 1404.8187 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 : 2.531 ------------------------------------------------------------------------------- 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: 2.9990 chunk 182 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3527 r_free = 0.3527 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104576 restraints weight = 23536.581| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.20 r_work: 0.3010 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.7679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 21720 Z= 0.241 Angle : 0.780 9.984 29304 Z= 0.396 Chirality : 0.056 0.158 3480 Planarity : 0.005 0.043 3720 Dihedral : 4.866 16.073 2880 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.83 % Allowed : 20.38 % Favored : 74.79 % 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: 2.02 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.80 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 59 HIS 0.007 0.002 HIS G 53 PHE 0.007 0.001 PHE W 124 TYR 0.009 0.002 TYR N 106 ARG 0.004 0.001 ARG D 93 Details of bonding type rmsd hydrogen bonds : bond 0.05511 ( 945) hydrogen bonds : angle 4.04552 ( 2331) covalent geometry : bond 0.00614 (21720) covalent geometry : angle 0.78000 (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 : 2.727 Fit side-chains REVERT: A 87 MET cc_start: 0.7577 (pmm) cc_final: 0.7365 (mmt) REVERT: A 101 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: A 123 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8446 (mttt) REVERT: A 142 LYS cc_start: 0.8285 (mttm) cc_final: 0.7990 (mptt) REVERT: P 87 MET cc_start: 0.7626 (pmm) cc_final: 0.7394 (mmt) REVERT: P 101 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: P 123 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8383 (mttp) REVERT: P 142 LYS cc_start: 0.8250 (mttm) cc_final: 0.7955 (mptt) REVERT: T 87 MET cc_start: 0.7576 (pmm) cc_final: 0.7366 (mmt) REVERT: T 101 GLU cc_start: 0.7938 (mp0) cc_final: 0.7270 (mm-30) REVERT: T 123 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8415 (mttt) REVERT: T 142 LYS cc_start: 0.8365 (mttm) cc_final: 0.8072 (mptt) REVERT: U 87 MET cc_start: 0.7645 (pmm) cc_final: 0.7429 (mmt) REVERT: U 101 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: U 123 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8376 (mttp) REVERT: U 142 LYS cc_start: 0.8280 (mttm) cc_final: 0.7981 (mptt) REVERT: E 102 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: E 104 GLU cc_start: 0.7715 (tp30) cc_final: 0.7397 (mm-30) REVERT: I 82 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7999 (ptpt) REVERT: I 101 GLU cc_start: 0.7941 (mp0) cc_final: 0.7283 (mm-30) REVERT: X 92 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: X 101 GLU cc_start: 0.7943 (mp0) cc_final: 0.7634 (mm-30) REVERT: X 142 LYS cc_start: 0.8306 (mttm) cc_final: 0.7991 (mptt) REVERT: D 36 GLN cc_start: 0.8344 (mt0) cc_final: 0.8128 (mt0) REVERT: D 78 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: D 93 ARG cc_start: 0.8574 (pmt170) cc_final: 0.8192 (pmt170) REVERT: D 110 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8446 (tttm) REVERT: D 142 LYS cc_start: 0.8327 (mttm) cc_final: 0.7971 (mptt) REVERT: F 49 GLU cc_start: 0.8663 (tt0) cc_final: 0.8436 (tt0) REVERT: F 78 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: F 110 LYS cc_start: 0.8903 (tttm) cc_final: 0.8464 (ttpt) REVERT: F 118 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: F 142 LYS cc_start: 0.8329 (mptt) cc_final: 0.8129 (mptt) REVERT: R 78 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: R 110 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8444 (tttm) REVERT: R 118 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: O 49 GLU cc_start: 0.8659 (tt0) cc_final: 0.8437 (tt0) REVERT: O 78 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: O 110 LYS cc_start: 0.8899 (tttm) cc_final: 0.8472 (ttpt) REVERT: O 118 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: O 142 LYS cc_start: 0.8331 (mptt) cc_final: 0.8130 (mptt) REVERT: C 78 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: C 110 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8517 (ttpt) REVERT: C 118 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: B 87 MET cc_start: 0.7464 (pmm) cc_final: 0.7136 (mmt) REVERT: B 101 GLU cc_start: 0.7954 (mp0) cc_final: 0.7598 (mm-30) REVERT: B 142 LYS cc_start: 0.8380 (mttm) cc_final: 0.8035 (mptt) REVERT: W 78 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: W 91 SER cc_start: 0.5454 (OUTLIER) cc_final: 0.5188 (t) REVERT: W 103 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7491 (tm-30) REVERT: W 110 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8439 (tttm) REVERT: W 125 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: K 102 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: K 104 GLU cc_start: 0.7690 (tp30) cc_final: 0.7380 (mm-30) REVERT: N 82 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7993 (ptpt) REVERT: N 101 GLU cc_start: 0.7947 (mp0) cc_final: 0.7281 (mm-30) REVERT: H 78 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: H 91 SER cc_start: 0.5507 (OUTLIER) cc_final: 0.5295 (t) REVERT: H 103 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7495 (tm-30) REVERT: H 110 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8324 (tttm) REVERT: L 78 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: L 102 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: L 104 GLU cc_start: 0.7698 (tp30) cc_final: 0.7456 (mm-30) REVERT: M 101 GLU cc_start: 0.7991 (mp0) cc_final: 0.7349 (mm-30) REVERT: Q 87 MET cc_start: 0.7391 (pmm) cc_final: 0.7047 (mmt) REVERT: Q 92 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: Q 101 GLU cc_start: 0.7920 (mp0) cc_final: 0.7640 (mm-30) REVERT: Q 142 LYS cc_start: 0.8355 (mttm) cc_final: 0.8021 (mptt) REVERT: J 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: J 101 GLU cc_start: 0.7938 (mp0) cc_final: 0.7230 (mm-30) REVERT: J 102 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: G 87 MET cc_start: 0.7431 (pmm) cc_final: 0.7134 (mmt) REVERT: G 101 GLU cc_start: 0.7953 (mp0) cc_final: 0.7611 (mm-30) REVERT: G 142 LYS cc_start: 0.8363 (mttm) cc_final: 0.8029 (mptt) REVERT: S 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: S 103 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7499 (tm-30) REVERT: S 110 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8339 (tttm) REVERT: V 78 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: V 104 GLU cc_start: 0.7717 (tp30) cc_final: 0.7468 (mm-30) REVERT: V 123 LYS cc_start: 0.8955 (mttm) cc_final: 0.8725 (mttt) outliers start: 116 outliers final: 44 residues processed: 654 average time/residue: 1.7405 time to fit residues: 1254.6909 Evaluate side-chains 625 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 552 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 116 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.132752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105851 restraints weight = 23642.769| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.26 r_work: 0.3065 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.7743 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= 0.147 Angle : 0.632 9.035 29304 Z= 0.318 Chirality : 0.053 0.148 3480 Planarity : 0.004 0.029 3720 Dihedral : 4.332 14.416 2880 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.96 % Allowed : 22.38 % Favored : 73.67 % 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: 2.16 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.12 (0.15), residues: 1392 loop : -0.61 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE I 124 TYR 0.008 0.002 TYR J 106 ARG 0.002 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 945) hydrogen bonds : angle 3.81606 ( 2331) covalent geometry : bond 0.00355 (21720) covalent geometry : angle 0.63236 (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 668 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 573 time to evaluate : 2.456 Fit side-chains REVERT: A 78 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: A 87 MET cc_start: 0.7540 (pmm) cc_final: 0.7304 (mmt) REVERT: A 101 GLU cc_start: 0.7764 (mp0) cc_final: 0.7214 (mm-30) REVERT: A 123 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8361 (mttp) REVERT: A 142 LYS cc_start: 0.8223 (mttm) cc_final: 0.7870 (mptt) REVERT: P 78 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: P 87 MET cc_start: 0.7556 (pmm) cc_final: 0.7334 (mmt) REVERT: P 101 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: P 103 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: P 123 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8319 (mttp) REVERT: P 142 LYS cc_start: 0.8175 (mttm) cc_final: 0.7832 (mptt) REVERT: T 78 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: T 87 MET cc_start: 0.7566 (pmm) cc_final: 0.7319 (mmt) REVERT: T 101 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: T 123 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8349 (mttp) REVERT: T 142 LYS cc_start: 0.8250 (mttm) cc_final: 0.7920 (mptt) REVERT: U 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: U 87 MET cc_start: 0.7560 (pmm) cc_final: 0.7329 (mmt) REVERT: U 101 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: U 103 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: U 123 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8319 (mttp) REVERT: U 142 LYS cc_start: 0.8211 (mttm) cc_final: 0.7855 (mptt) REVERT: E 78 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: E 102 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: E 103 GLU cc_start: 0.7745 (tp30) cc_final: 0.7460 (tm-30) REVERT: I 101 GLU cc_start: 0.7874 (mp0) cc_final: 0.7265 (mm-30) REVERT: X 87 MET cc_start: 0.7407 (pmm) cc_final: 0.7044 (mmt) REVERT: X 92 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: X 101 GLU cc_start: 0.7928 (mp0) cc_final: 0.7587 (mm-30) REVERT: X 142 LYS cc_start: 0.8190 (mttm) cc_final: 0.7846 (mptt) REVERT: D 36 GLN cc_start: 0.8190 (mt0) cc_final: 0.7918 (tt0) REVERT: D 91 SER cc_start: 0.5302 (OUTLIER) cc_final: 0.5053 (t) REVERT: D 110 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8368 (ttpt) REVERT: D 142 LYS cc_start: 0.8190 (mttm) cc_final: 0.7824 (mptt) REVERT: F 78 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: F 110 LYS cc_start: 0.8849 (tttm) cc_final: 0.8398 (ttpt) REVERT: F 118 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: R 78 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: R 110 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8417 (ttpt) REVERT: R 118 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: O 78 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: O 110 LYS cc_start: 0.8842 (tttm) cc_final: 0.8393 (ttpt) REVERT: O 118 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: C 78 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: C 101 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: C 110 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8350 (tttm) REVERT: C 118 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: B 87 MET cc_start: 0.7439 (pmm) cc_final: 0.7069 (mmt) REVERT: B 101 GLU cc_start: 0.7925 (mp0) cc_final: 0.7559 (mm-30) REVERT: B 142 LYS cc_start: 0.8236 (mttm) cc_final: 0.7858 (mptt) REVERT: W 78 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: W 91 SER cc_start: 0.5232 (OUTLIER) cc_final: 0.5010 (t) REVERT: W 103 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7319 (tm-30) REVERT: W 110 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8202 (tttm) REVERT: W 125 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: K 78 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: K 102 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: K 103 GLU cc_start: 0.7724 (tp30) cc_final: 0.7438 (tm-30) REVERT: N 101 GLU cc_start: 0.7869 (mp0) cc_final: 0.7262 (mm-30) REVERT: H 78 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: H 91 SER cc_start: 0.5376 (OUTLIER) cc_final: 0.5146 (t) REVERT: H 103 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7290 (tm-30) REVERT: H 110 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8256 (tttm) REVERT: L 49 GLU cc_start: 0.8564 (tt0) cc_final: 0.8304 (tt0) REVERT: L 78 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: L 104 GLU cc_start: 0.7625 (tp30) cc_final: 0.7402 (mm-30) REVERT: M 49 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: M 101 GLU cc_start: 0.7939 (mp0) cc_final: 0.7359 (mm-30) REVERT: M 102 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: Q 87 MET cc_start: 0.7378 (pmm) cc_final: 0.6994 (mmt) REVERT: Q 92 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: Q 101 GLU cc_start: 0.7891 (mp0) cc_final: 0.7599 (mm-30) REVERT: Q 142 LYS cc_start: 0.8220 (mttm) cc_final: 0.7863 (mptt) REVERT: J 78 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: J 82 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7859 (ptpt) REVERT: J 101 GLU cc_start: 0.7946 (mp0) cc_final: 0.7278 (mm-30) REVERT: G 87 MET cc_start: 0.7388 (pmm) cc_final: 0.7064 (mmt) REVERT: G 101 GLU cc_start: 0.7929 (mp0) cc_final: 0.7569 (mm-30) REVERT: G 142 LYS cc_start: 0.8260 (mttm) cc_final: 0.7909 (mptt) REVERT: S 78 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: S 103 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7349 (tm-30) REVERT: S 110 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8185 (tttm) REVERT: V 78 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: V 104 GLU cc_start: 0.7688 (tp30) cc_final: 0.7466 (mm-30) outliers start: 95 outliers final: 31 residues processed: 643 average time/residue: 1.6505 time to fit residues: 1175.5048 Evaluate side-chains 626 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 557 time to evaluate : 4.212 ------------------------------------------------------------------------------- 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 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 G residue 139 SER 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: 6.9990 chunk 167 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.133621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107473 restraints weight = 23657.720| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.20 r_work: 0.3056 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 21720 Z= 0.123 Angle : 0.586 8.599 29304 Z= 0.294 Chirality : 0.052 0.144 3480 Planarity : 0.003 0.026 3720 Dihedral : 4.070 13.309 2880 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.71 % Allowed : 23.92 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.27 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.13 (0.15), residues: 1392 loop : -0.46 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE M 124 TYR 0.010 0.002 TYR K 106 ARG 0.001 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 945) hydrogen bonds : angle 3.77890 ( 2331) covalent geometry : bond 0.00289 (21720) covalent geometry : angle 0.58566 (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 659 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 570 time to evaluate : 2.809 Fit side-chains REVERT: A 37 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8628 (mm) REVERT: A 49 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: A 78 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: A 87 MET cc_start: 0.7538 (pmm) cc_final: 0.7279 (mmt) REVERT: A 101 GLU cc_start: 0.7776 (mp0) cc_final: 0.7257 (mm-30) REVERT: A 123 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8403 (mttp) REVERT: A 142 LYS cc_start: 0.8186 (mttm) cc_final: 0.7880 (mptt) REVERT: P 78 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: P 87 MET cc_start: 0.7557 (pmm) cc_final: 0.7294 (mmt) REVERT: P 101 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: P 103 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: P 123 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8382 (mttt) REVERT: P 142 LYS cc_start: 0.8190 (mttm) cc_final: 0.7878 (mptt) REVERT: T 78 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: T 87 MET cc_start: 0.7559 (pmm) cc_final: 0.7274 (mmt) REVERT: T 101 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: T 123 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8378 (mttt) REVERT: T 142 LYS cc_start: 0.8189 (mttm) cc_final: 0.7906 (mptt) REVERT: U 78 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: U 87 MET cc_start: 0.7571 (pmm) cc_final: 0.7310 (mmt) REVERT: U 101 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: U 103 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: U 123 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8389 (mttt) REVERT: U 142 LYS cc_start: 0.8201 (mttm) cc_final: 0.7883 (mptt) REVERT: E 49 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: E 78 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: E 102 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: E 110 LYS cc_start: 0.8950 (tttm) cc_final: 0.8691 (tttm) REVERT: I 101 GLU cc_start: 0.7906 (mp0) cc_final: 0.7339 (mm-30) REVERT: I 102 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: X 87 MET cc_start: 0.7388 (pmm) cc_final: 0.7009 (mmt) REVERT: X 101 GLU cc_start: 0.7954 (mp0) cc_final: 0.7605 (mm-30) REVERT: X 142 LYS cc_start: 0.8153 (mttm) cc_final: 0.7863 (mptt) REVERT: D 36 GLN cc_start: 0.8186 (mt0) cc_final: 0.7949 (tt0) REVERT: D 78 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: D 91 SER cc_start: 0.5258 (OUTLIER) cc_final: 0.5028 (t) REVERT: D 110 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8384 (ttpt) REVERT: D 142 LYS cc_start: 0.8174 (mttm) cc_final: 0.7848 (mptt) REVERT: F 78 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: F 110 LYS cc_start: 0.8863 (tttm) cc_final: 0.8454 (ttpt) REVERT: F 118 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: R 78 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: R 110 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8473 (ttpt) REVERT: R 118 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: O 78 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: O 110 LYS cc_start: 0.8848 (tttm) cc_final: 0.8447 (ttpt) REVERT: O 118 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: C 78 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: C 101 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: C 110 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8435 (ttpt) REVERT: C 118 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: B 87 MET cc_start: 0.7429 (pmm) cc_final: 0.7049 (mmt) REVERT: B 101 GLU cc_start: 0.7958 (mp0) cc_final: 0.7606 (mm-30) REVERT: B 142 LYS cc_start: 0.8245 (mttm) cc_final: 0.7921 (mptt) REVERT: W 78 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: W 91 SER cc_start: 0.5222 (OUTLIER) cc_final: 0.5014 (t) REVERT: W 103 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7296 (tm-30) REVERT: W 110 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8233 (tttm) REVERT: W 125 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: K 49 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: K 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: K 102 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: N 101 GLU cc_start: 0.7926 (mp0) cc_final: 0.7349 (mm-30) REVERT: N 102 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: H 78 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: H 91 SER cc_start: 0.5329 (OUTLIER) cc_final: 0.5128 (t) REVERT: H 103 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7331 (tm-30) REVERT: H 110 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8243 (tttm) REVERT: L 49 GLU cc_start: 0.8561 (tt0) cc_final: 0.8314 (tt0) REVERT: L 104 GLU cc_start: 0.7642 (tp30) cc_final: 0.7425 (mm-30) REVERT: L 110 LYS cc_start: 0.8958 (tttm) cc_final: 0.8699 (tttm) REVERT: M 101 GLU cc_start: 0.7951 (mp0) cc_final: 0.7429 (mm-30) REVERT: M 102 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: Q 87 MET cc_start: 0.7409 (pmm) cc_final: 0.6992 (mmt) REVERT: Q 101 GLU cc_start: 0.7894 (mp0) cc_final: 0.7629 (mm-30) REVERT: Q 142 LYS cc_start: 0.8227 (mttm) cc_final: 0.7917 (mptt) REVERT: J 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: J 101 GLU cc_start: 0.7916 (mp0) cc_final: 0.7331 (mm-30) REVERT: J 102 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: G 87 MET cc_start: 0.7412 (pmm) cc_final: 0.7047 (mmt) REVERT: G 101 GLU cc_start: 0.7956 (mp0) cc_final: 0.7614 (mm-30) REVERT: G 142 LYS cc_start: 0.8239 (mttm) cc_final: 0.7933 (mptt) REVERT: S 78 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: S 103 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7421 (tm-30) REVERT: S 110 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8219 (tttm) REVERT: V 78 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8321 (tm-30) REVERT: V 110 LYS cc_start: 0.8951 (tttm) cc_final: 0.8690 (tttm) outliers start: 89 outliers final: 42 residues processed: 635 average time/residue: 1.6162 time to fit residues: 1137.6867 Evaluate side-chains 658 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 574 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 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 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 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 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 102 GLU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 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 H residue 91 SER Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 145 ASN 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 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: 2.9990 chunk 215 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 123 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 = 0.132128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105163 restraints weight = 23358.320| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.24 r_work: 0.3016 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 21720 Z= 0.155 Angle : 0.635 8.965 29304 Z= 0.319 Chirality : 0.053 0.147 3480 Planarity : 0.004 0.030 3720 Dihedral : 4.247 13.317 2880 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.50 % Allowed : 23.46 % Favored : 72.04 % 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: 2.21 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.07 (0.15), residues: 1392 loop : -0.46 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP W 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE J 124 TYR 0.009 0.002 TYR U 106 ARG 0.002 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 945) hydrogen bonds : angle 3.86865 ( 2331) covalent geometry : bond 0.00378 (21720) covalent geometry : angle 0.63521 (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 671 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 563 time to evaluate : 2.649 Fit side-chains REVERT: A 37 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8633 (mm) REVERT: A 78 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: A 87 MET cc_start: 0.7490 (pmm) cc_final: 0.7285 (mmt) REVERT: A 101 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: A 123 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8390 (mttp) REVERT: A 142 LYS cc_start: 0.8219 (mttm) cc_final: 0.7881 (mptt) REVERT: P 78 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: P 87 MET cc_start: 0.7537 (pmm) cc_final: 0.7281 (mmt) REVERT: P 101 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: P 103 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: P 123 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8339 (mttt) REVERT: P 142 LYS cc_start: 0.8195 (mttm) cc_final: 0.7858 (mptt) REVERT: T 78 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: T 87 MET cc_start: 0.7517 (pmm) cc_final: 0.7286 (mmt) REVERT: T 101 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: T 123 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8347 (mttp) REVERT: T 142 LYS cc_start: 0.8241 (mttm) cc_final: 0.7930 (mptt) REVERT: U 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: U 87 MET cc_start: 0.7537 (pmm) cc_final: 0.7276 (mmt) REVERT: U 101 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: U 103 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: U 123 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8326 (mttt) REVERT: U 142 LYS cc_start: 0.8199 (mttm) cc_final: 0.7863 (mptt) REVERT: E 78 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: E 102 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: E 110 LYS cc_start: 0.8922 (tttm) cc_final: 0.8646 (tttm) REVERT: I 101 GLU cc_start: 0.7940 (mp0) cc_final: 0.7459 (mm-30) REVERT: I 102 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: X 87 MET cc_start: 0.7402 (pmm) cc_final: 0.7044 (mmt) REVERT: X 92 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7982 (mt-10) REVERT: X 101 GLU cc_start: 0.7935 (mp0) cc_final: 0.7595 (mm-30) REVERT: X 142 LYS cc_start: 0.8194 (mttm) cc_final: 0.7860 (mptt) REVERT: D 36 GLN cc_start: 0.8223 (mt0) cc_final: 0.7988 (tt0) REVERT: D 78 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: D 91 SER cc_start: 0.5252 (OUTLIER) cc_final: 0.5034 (t) REVERT: D 103 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 110 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8369 (ttpt) REVERT: D 142 LYS cc_start: 0.8199 (mttm) cc_final: 0.7858 (mptt) REVERT: F 78 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: F 110 LYS cc_start: 0.8835 (tttm) cc_final: 0.8393 (ttpt) REVERT: F 118 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: R 78 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: R 110 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8412 (ttpt) REVERT: R 118 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: O 78 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: O 110 LYS cc_start: 0.8840 (tttm) cc_final: 0.8400 (ttpt) REVERT: O 118 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: C 78 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: C 110 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8407 (ttpt) REVERT: C 118 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 87 MET cc_start: 0.7447 (pmm) cc_final: 0.7075 (mmt) REVERT: B 101 GLU cc_start: 0.7930 (mp0) cc_final: 0.7569 (mm-30) REVERT: B 142 LYS cc_start: 0.8309 (mttm) cc_final: 0.7953 (mptt) REVERT: W 49 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: W 78 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: W 103 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7254 (tm-30) REVERT: W 110 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8332 (tttm) REVERT: W 125 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: K 78 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: K 102 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: N 101 GLU cc_start: 0.7941 (mp0) cc_final: 0.7455 (mm-30) REVERT: N 102 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: H 78 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: H 103 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7343 (tm-30) REVERT: H 110 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8288 (tttm) REVERT: L 49 GLU cc_start: 0.8564 (tt0) cc_final: 0.8318 (tt0) REVERT: L 78 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: L 104 GLU cc_start: 0.7585 (tp30) cc_final: 0.7360 (mm-30) REVERT: M 101 GLU cc_start: 0.7942 (mp0) cc_final: 0.7474 (mm-30) REVERT: M 102 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: Q 87 MET cc_start: 0.7400 (pmm) cc_final: 0.7031 (mmt) REVERT: Q 101 GLU cc_start: 0.7898 (mp0) cc_final: 0.7601 (mm-30) REVERT: Q 142 LYS cc_start: 0.8251 (mttm) cc_final: 0.7907 (mptt) REVERT: J 78 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: J 101 GLU cc_start: 0.7922 (mp0) cc_final: 0.7356 (mm-30) REVERT: J 102 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: G 87 MET cc_start: 0.7396 (pmm) cc_final: 0.7059 (mmt) REVERT: G 101 GLU cc_start: 0.7917 (mp0) cc_final: 0.7576 (mm-30) REVERT: G 142 LYS cc_start: 0.8274 (mttm) cc_final: 0.7936 (mptt) REVERT: S 78 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: S 102 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: S 103 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7376 (tm-30) REVERT: S 110 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8312 (tttm) REVERT: V 78 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8304 (tm-30) outliers start: 108 outliers final: 46 residues processed: 634 average time/residue: 1.6782 time to fit residues: 1174.7627 Evaluate side-chains 647 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 561 time to evaluate : 2.624 ------------------------------------------------------------------------------- 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 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 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 91 SER 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 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 49 GLU 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 181 optimal weight: 0.0020 chunk 221 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.132864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106011 restraints weight = 23408.547| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.24 r_work: 0.3068 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 21720 Z= 0.134 Angle : 0.600 8.724 29304 Z= 0.301 Chirality : 0.053 0.145 3480 Planarity : 0.003 0.028 3720 Dihedral : 4.098 13.145 2880 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 5.17 % Allowed : 23.29 % Favored : 71.54 % 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: 2.29 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.08 (0.15), residues: 1392 loop : -0.35 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 59 HIS 0.002 0.001 HIS T 53 PHE 0.005 0.001 PHE N 124 TYR 0.010 0.002 TYR A 106 ARG 0.001 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 945) hydrogen bonds : angle 3.80653 ( 2331) covalent geometry : bond 0.00320 (21720) covalent geometry : angle 0.60044 (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 705 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 581 time to evaluate : 2.582 Fit side-chains REVERT: A 37 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8612 (mm) REVERT: A 49 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: A 78 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: A 87 MET cc_start: 0.7487 (pmm) cc_final: 0.7273 (mmt) REVERT: A 101 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: A 123 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8363 (mttp) REVERT: A 142 LYS cc_start: 0.8189 (mttm) cc_final: 0.7865 (mptt) REVERT: P 49 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: P 78 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: P 87 MET cc_start: 0.7544 (pmm) cc_final: 0.7292 (mmt) REVERT: P 101 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: P 103 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: P 123 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8352 (mttt) REVERT: P 142 LYS cc_start: 0.8157 (mttm) cc_final: 0.7841 (mptt) REVERT: T 78 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: T 87 MET cc_start: 0.7535 (pmm) cc_final: 0.7281 (mmt) REVERT: T 101 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: T 123 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8367 (mttt) REVERT: T 142 LYS cc_start: 0.8159 (mttm) cc_final: 0.7852 (mptt) REVERT: U 49 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: U 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: U 87 MET cc_start: 0.7537 (pmm) cc_final: 0.7279 (mmt) REVERT: U 101 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: U 103 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: U 123 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8338 (mttt) REVERT: U 142 LYS cc_start: 0.8164 (mttm) cc_final: 0.7839 (mptt) REVERT: E 49 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: E 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: E 102 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: E 110 LYS cc_start: 0.8913 (tttm) cc_final: 0.8635 (tttm) REVERT: I 49 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: I 101 GLU cc_start: 0.7922 (mp0) cc_final: 0.7442 (mm-30) REVERT: I 102 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: X 87 MET cc_start: 0.7389 (pmm) cc_final: 0.7022 (mmt) REVERT: X 92 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7931 (mt-10) REVERT: X 101 GLU cc_start: 0.7919 (mp0) cc_final: 0.7568 (mm-30) REVERT: X 142 LYS cc_start: 0.8141 (mttm) cc_final: 0.7811 (mptt) REVERT: D 36 GLN cc_start: 0.8183 (mt0) cc_final: 0.7947 (tt0) REVERT: D 78 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: D 110 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8344 (ttpt) REVERT: D 142 LYS cc_start: 0.8163 (mttm) cc_final: 0.7816 (mptt) REVERT: F 78 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: F 110 LYS cc_start: 0.8823 (tttm) cc_final: 0.8380 (ttpt) REVERT: F 118 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: R 49 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: R 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: R 110 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8393 (ttpt) REVERT: R 118 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: O 78 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: O 110 LYS cc_start: 0.8825 (tttm) cc_final: 0.8386 (ttpt) REVERT: O 118 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: C 49 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: C 78 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: C 101 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: C 110 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8392 (ttpt) REVERT: C 118 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: B 87 MET cc_start: 0.7442 (pmm) cc_final: 0.7077 (mmt) REVERT: B 101 GLU cc_start: 0.7935 (mp0) cc_final: 0.7578 (mm-30) REVERT: B 142 LYS cc_start: 0.8263 (mttm) cc_final: 0.7907 (mptt) REVERT: W 49 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: W 78 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: W 102 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: W 103 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7286 (tm-30) REVERT: W 110 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8313 (tttm) REVERT: W 125 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: K 49 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: K 78 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: K 102 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: N 49 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: N 101 GLU cc_start: 0.7914 (mp0) cc_final: 0.7435 (mm-30) REVERT: N 102 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: H 78 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: H 102 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: H 103 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7264 (tm-30) REVERT: H 110 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8267 (tttm) REVERT: L 49 GLU cc_start: 0.8550 (tt0) cc_final: 0.8301 (tt0) REVERT: L 78 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: L 104 GLU cc_start: 0.7557 (tp30) cc_final: 0.7348 (mm-30) REVERT: L 110 LYS cc_start: 0.8922 (tttm) cc_final: 0.8652 (tttm) REVERT: M 49 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: M 101 GLU cc_start: 0.7934 (mp0) cc_final: 0.7467 (mm-30) REVERT: M 102 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: Q 87 MET cc_start: 0.7398 (pmm) cc_final: 0.7017 (mmt) REVERT: Q 92 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: Q 101 GLU cc_start: 0.7905 (mp0) cc_final: 0.7614 (mm-30) REVERT: Q 142 LYS cc_start: 0.8213 (mttm) cc_final: 0.7866 (mptt) REVERT: J 49 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: J 78 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: J 101 GLU cc_start: 0.7929 (mp0) cc_final: 0.7388 (mm-30) REVERT: J 102 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: G 87 MET cc_start: 0.7420 (pmm) cc_final: 0.7071 (mmt) REVERT: G 101 GLU cc_start: 0.7926 (mp0) cc_final: 0.7591 (mm-30) REVERT: G 142 LYS cc_start: 0.8223 (mttm) cc_final: 0.7877 (mptt) REVERT: S 78 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: S 102 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: S 103 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7337 (tm-30) REVERT: S 110 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8293 (tttm) REVERT: V 78 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: V 110 LYS cc_start: 0.8910 (tttm) cc_final: 0.8639 (tttm) outliers start: 124 outliers final: 60 residues processed: 651 average time/residue: 1.7554 time to fit residues: 1267.7569 Evaluate side-chains 694 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 580 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 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 49 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 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 121 SER Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 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 D residue 102 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 49 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 49 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 121 SER 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 49 GLU 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 49 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 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 92 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 49 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 J residue 121 SER Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 121 SER 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 102 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 198 optimal weight: 0.0870 chunk 250 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106806 restraints weight = 23602.545| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.25 r_work: 0.3080 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 21720 Z= 0.116 Angle : 0.573 8.595 29304 Z= 0.287 Chirality : 0.052 0.145 3480 Planarity : 0.003 0.025 3720 Dihedral : 3.963 12.928 2880 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 5.00 % Allowed : 23.75 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.34 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.06 (0.15), residues: 1392 loop : -0.26 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE N 124 TYR 0.010 0.001 TYR U 106 ARG 0.001 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 945) hydrogen bonds : angle 3.77318 ( 2331) covalent geometry : bond 0.00270 (21720) covalent geometry : angle 0.57339 (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 693 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 573 time to evaluate : 2.454 Fit side-chains REVERT: A 49 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: A 78 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: A 87 MET cc_start: 0.7473 (pmm) cc_final: 0.7238 (mmt) REVERT: A 101 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7355 (mm-30) REVERT: A 123 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8389 (mttt) REVERT: A 142 LYS cc_start: 0.8163 (mttm) cc_final: 0.7850 (mptt) REVERT: P 49 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: P 78 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: P 87 MET cc_start: 0.7522 (pmm) cc_final: 0.7278 (mmt) REVERT: P 101 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: P 103 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: P 123 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8359 (mttt) REVERT: P 142 LYS cc_start: 0.8132 (mttm) cc_final: 0.7824 (mptt) REVERT: T 78 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: T 87 MET cc_start: 0.7532 (pmm) cc_final: 0.7263 (mmt) REVERT: T 101 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: T 123 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8355 (mttt) REVERT: T 142 LYS cc_start: 0.8144 (mttm) cc_final: 0.7854 (mptt) REVERT: U 49 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: U 78 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: U 87 MET cc_start: 0.7540 (pmm) cc_final: 0.7263 (mmt) REVERT: U 101 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: U 103 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: U 123 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8333 (mttt) REVERT: U 142 LYS cc_start: 0.8131 (mttm) cc_final: 0.7817 (mptt) REVERT: E 49 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: E 78 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: E 102 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: E 110 LYS cc_start: 0.8902 (tttm) cc_final: 0.8621 (tttm) REVERT: I 49 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: I 101 GLU cc_start: 0.7927 (mp0) cc_final: 0.7449 (mm-30) REVERT: I 102 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: X 87 MET cc_start: 0.7382 (pmm) cc_final: 0.6987 (mmt) REVERT: X 92 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7917 (mt-10) REVERT: X 101 GLU cc_start: 0.7910 (mp0) cc_final: 0.7568 (mm-30) REVERT: X 142 LYS cc_start: 0.8115 (mttm) cc_final: 0.7794 (mptt) REVERT: D 78 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: D 110 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8160 (tttm) REVERT: D 142 LYS cc_start: 0.8111 (mttm) cc_final: 0.7771 (mptt) REVERT: F 78 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: F 101 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: F 110 LYS cc_start: 0.8828 (tttm) cc_final: 0.8304 (tttm) REVERT: F 118 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: R 49 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: R 78 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: R 110 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8391 (ttpt) REVERT: R 118 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: O 78 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: O 101 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: O 110 LYS cc_start: 0.8815 (tttm) cc_final: 0.8300 (tttm) REVERT: O 118 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: O 142 LYS cc_start: 0.8163 (mptt) cc_final: 0.7749 (mptt) REVERT: C 49 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: C 78 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: C 101 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: C 110 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8397 (ttpt) REVERT: C 118 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: B 87 MET cc_start: 0.7414 (pmm) cc_final: 0.7043 (mmt) REVERT: B 101 GLU cc_start: 0.7922 (mp0) cc_final: 0.7572 (mm-30) REVERT: B 142 LYS cc_start: 0.8212 (mttm) cc_final: 0.7886 (mptt) REVERT: W 49 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: W 78 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: W 102 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: W 103 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7285 (tm-30) REVERT: W 110 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8178 (tttm) REVERT: W 125 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: K 49 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: K 78 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8218 (tm-30) REVERT: K 102 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: N 49 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: N 101 GLU cc_start: 0.7916 (mp0) cc_final: 0.7440 (mm-30) REVERT: N 102 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: H 78 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: H 102 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: H 103 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7283 (tm-30) REVERT: H 110 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8133 (tttm) REVERT: L 49 GLU cc_start: 0.8548 (tt0) cc_final: 0.8300 (tt0) REVERT: L 78 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: L 104 GLU cc_start: 0.7532 (tp30) cc_final: 0.7315 (mm-30) REVERT: L 110 LYS cc_start: 0.8907 (tttm) cc_final: 0.8636 (tttm) REVERT: M 49 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: M 101 GLU cc_start: 0.7938 (mp0) cc_final: 0.7457 (mm-30) REVERT: M 102 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: Q 49 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: Q 87 MET cc_start: 0.7364 (pmm) cc_final: 0.6983 (mmt) REVERT: Q 92 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: Q 101 GLU cc_start: 0.7879 (mp0) cc_final: 0.7599 (mm-30) REVERT: Q 142 LYS cc_start: 0.8175 (mttm) cc_final: 0.7839 (mptt) REVERT: J 78 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: J 101 GLU cc_start: 0.7922 (mp0) cc_final: 0.7391 (mm-30) REVERT: J 102 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: G 87 MET cc_start: 0.7400 (pmm) cc_final: 0.7040 (mmt) REVERT: G 101 GLU cc_start: 0.7916 (mp0) cc_final: 0.7583 (mm-30) REVERT: G 142 LYS cc_start: 0.8180 (mttm) cc_final: 0.7850 (mptt) REVERT: S 78 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: S 103 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7296 (tm-30) REVERT: S 110 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8161 (tttm) REVERT: V 78 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: V 110 LYS cc_start: 0.8908 (tttm) cc_final: 0.8636 (tttm) outliers start: 120 outliers final: 63 residues processed: 646 average time/residue: 1.6826 time to fit residues: 1204.4308 Evaluate side-chains 688 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 571 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 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 49 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 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 121 SER Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 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 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 R residue 49 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 49 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 121 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 49 GLU 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 121 SER Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain 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 49 GLU Chi-restraints excluded: chain Q residue 92 GLU 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 121 SER Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 121 SER 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 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 Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 192 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 126 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111043 restraints weight = 23473.856| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.19 r_work: 0.3133 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.7833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 21720 Z= 0.084 Angle : 0.512 7.861 29304 Z= 0.256 Chirality : 0.051 0.142 3480 Planarity : 0.003 0.023 3720 Dihedral : 3.618 12.418 2880 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.67 % Allowed : 25.17 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.58 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.15 (0.15), residues: 1392 loop : 0.01 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 59 HIS 0.002 0.000 HIS T 53 PHE 0.004 0.001 PHE M 124 TYR 0.010 0.001 TYR A 106 ARG 0.001 0.000 ARG T 107 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 945) hydrogen bonds : angle 3.70085 ( 2331) covalent geometry : bond 0.00183 (21720) covalent geometry : angle 0.51161 (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 662 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 574 time to evaluate : 2.700 Fit side-chains REVERT: A 78 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: A 87 MET cc_start: 0.7408 (pmm) cc_final: 0.7144 (mmt) REVERT: A 101 GLU cc_start: 0.7769 (mp0) cc_final: 0.7400 (mm-30) REVERT: A 123 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8406 (mttt) REVERT: A 142 LYS cc_start: 0.8072 (mttm) cc_final: 0.7787 (mptt) REVERT: P 78 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: P 87 MET cc_start: 0.7502 (pmm) cc_final: 0.7232 (mmt) REVERT: P 101 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7181 (mm-30) REVERT: P 103 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: P 123 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8381 (mttt) REVERT: P 142 LYS cc_start: 0.8041 (mttm) cc_final: 0.7753 (mptt) REVERT: T 87 MET cc_start: 0.7424 (pmm) cc_final: 0.7154 (mmt) REVERT: T 101 GLU cc_start: 0.7836 (mp0) cc_final: 0.7326 (mm-30) REVERT: T 110 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8467 (tttm) REVERT: T 123 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8346 (mttt) REVERT: T 142 LYS cc_start: 0.8099 (mttm) cc_final: 0.7854 (mptt) REVERT: U 78 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: U 87 MET cc_start: 0.7504 (pmm) cc_final: 0.7218 (mmt) REVERT: U 101 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: U 103 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: U 123 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8369 (mttt) REVERT: U 142 LYS cc_start: 0.8037 (mttm) cc_final: 0.7743 (mptt) REVERT: E 78 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: E 110 LYS cc_start: 0.8894 (tttm) cc_final: 0.8623 (tttm) REVERT: I 101 GLU cc_start: 0.7916 (mp0) cc_final: 0.7448 (mm-30) REVERT: I 142 LYS cc_start: 0.8073 (mptt) cc_final: 0.7740 (mptt) REVERT: X 92 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7913 (mt-10) REVERT: X 101 GLU cc_start: 0.7914 (mp0) cc_final: 0.7590 (mm-30) REVERT: X 142 LYS cc_start: 0.8050 (mttm) cc_final: 0.7778 (mptt) REVERT: D 78 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: D 110 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8156 (tttm) REVERT: D 142 LYS cc_start: 0.8003 (mttm) cc_final: 0.7698 (mptt) REVERT: F 101 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: F 110 LYS cc_start: 0.8789 (tttm) cc_final: 0.8411 (ttpt) REVERT: F 118 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: R 110 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8389 (ttpt) REVERT: R 118 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: O 101 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: O 110 LYS cc_start: 0.8768 (tttm) cc_final: 0.8409 (ttpt) REVERT: O 118 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: C 101 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: C 110 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8415 (ttpt) REVERT: C 118 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: B 87 MET cc_start: 0.7379 (pmm) cc_final: 0.6936 (mmt) REVERT: B 101 GLU cc_start: 0.7918 (mp0) cc_final: 0.7569 (mm-30) REVERT: B 142 LYS cc_start: 0.8111 (mttm) cc_final: 0.7866 (mptt) REVERT: W 78 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: W 103 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7278 (tm-30) REVERT: W 110 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8199 (tttm) REVERT: W 125 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: W 142 LYS cc_start: 0.8068 (mptt) cc_final: 0.7842 (mptt) REVERT: K 78 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: N 101 GLU cc_start: 0.7900 (mp0) cc_final: 0.7450 (mm-30) REVERT: N 142 LYS cc_start: 0.8067 (mptt) cc_final: 0.7736 (mptt) REVERT: H 78 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: H 103 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7264 (tm-30) REVERT: H 110 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8146 (tttm) REVERT: L 49 GLU cc_start: 0.8506 (tt0) cc_final: 0.8275 (tt0) REVERT: L 78 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: L 110 LYS cc_start: 0.8912 (tttm) cc_final: 0.8649 (tttm) REVERT: M 101 GLU cc_start: 0.7922 (mp0) cc_final: 0.7441 (mm-30) REVERT: Q 49 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: Q 87 MET cc_start: 0.7334 (pmm) cc_final: 0.6884 (mmt) REVERT: Q 92 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: Q 101 GLU cc_start: 0.7850 (mp0) cc_final: 0.7576 (mm-30) REVERT: Q 142 LYS cc_start: 0.8091 (mttm) cc_final: 0.7853 (mptt) REVERT: J 101 GLU cc_start: 0.7900 (mp0) cc_final: 0.7356 (mm-30) REVERT: J 102 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: J 142 LYS cc_start: 0.8072 (mptt) cc_final: 0.7775 (mptt) REVERT: G 87 MET cc_start: 0.7342 (pmm) cc_final: 0.6920 (mmt) REVERT: G 101 GLU cc_start: 0.7913 (mp0) cc_final: 0.7592 (mm-30) REVERT: G 142 LYS cc_start: 0.8102 (mttm) cc_final: 0.7869 (mptt) REVERT: S 78 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: S 103 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7297 (tm-30) REVERT: S 110 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8171 (tttm) REVERT: V 78 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: V 110 LYS cc_start: 0.8891 (tttm) cc_final: 0.8623 (tttm) outliers start: 88 outliers final: 36 residues processed: 622 average time/residue: 1.5391 time to fit residues: 1064.6434 Evaluate side-chains 624 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 560 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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 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 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 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 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 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 145 ASN Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 145 ASN Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 78 GLU 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 30 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 113 optimal weight: 0.2980 chunk 208 optimal weight: 0.9980 chunk 191 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.134941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108954 restraints weight = 23602.940| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.18 r_work: 0.3097 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 21720 Z= 0.110 Angle : 0.558 8.211 29304 Z= 0.279 Chirality : 0.052 0.142 3480 Planarity : 0.003 0.025 3720 Dihedral : 3.755 12.646 2880 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.79 % Allowed : 26.12 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.13 (0.15), residues: 1392 loop : -0.02 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP S 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE N 124 TYR 0.011 0.001 TYR D 106 ARG 0.001 0.000 ARG T 107 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 945) hydrogen bonds : angle 3.74175 ( 2331) covalent geometry : bond 0.00255 (21720) covalent geometry : angle 0.55838 (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 622 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 555 time to evaluate : 2.783 Fit side-chains REVERT: A 78 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: A 87 MET cc_start: 0.7443 (pmm) cc_final: 0.7199 (mmt) REVERT: A 101 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: A 123 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8449 (mttt) REVERT: A 142 LYS cc_start: 0.8128 (mttm) cc_final: 0.7854 (mptt) REVERT: P 78 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: P 87 MET cc_start: 0.7502 (pmm) cc_final: 0.7271 (mmt) REVERT: P 101 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: P 103 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: P 123 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8397 (mttt) REVERT: P 142 LYS cc_start: 0.8106 (mttm) cc_final: 0.7825 (mptt) REVERT: T 78 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: T 87 MET cc_start: 0.7479 (pmm) cc_final: 0.7231 (mmt) REVERT: T 101 GLU cc_start: 0.7841 (mp0) cc_final: 0.7370 (mm-30) REVERT: T 123 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8421 (mttt) REVERT: T 142 LYS cc_start: 0.8171 (mttm) cc_final: 0.7934 (mptt) REVERT: U 78 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: U 87 MET cc_start: 0.7512 (pmm) cc_final: 0.7254 (mmt) REVERT: U 101 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: U 103 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: U 123 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8382 (mttt) REVERT: U 142 LYS cc_start: 0.8102 (mttm) cc_final: 0.7821 (mptt) REVERT: E 78 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: E 110 LYS cc_start: 0.8941 (tttm) cc_final: 0.8669 (tttm) REVERT: I 101 GLU cc_start: 0.7914 (mp0) cc_final: 0.7480 (mm-30) REVERT: X 87 MET cc_start: 0.7390 (pmm) cc_final: 0.6953 (mmt) REVERT: X 92 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7962 (mt-10) REVERT: X 101 GLU cc_start: 0.7944 (mp0) cc_final: 0.7622 (mm-30) REVERT: X 142 LYS cc_start: 0.8133 (mttm) cc_final: 0.7887 (mptt) REVERT: D 78 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: D 110 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8221 (tttm) REVERT: D 142 LYS cc_start: 0.8090 (mttm) cc_final: 0.7803 (mptt) REVERT: F 78 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: F 101 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: F 110 LYS cc_start: 0.8820 (tttm) cc_final: 0.8364 (tttm) REVERT: F 118 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: R 78 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: R 110 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8445 (ttpt) REVERT: R 118 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: O 78 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: O 101 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: O 110 LYS cc_start: 0.8805 (tttm) cc_final: 0.8369 (tttm) REVERT: O 118 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 78 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: C 101 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: C 110 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8471 (ttpt) REVERT: C 118 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: B 87 MET cc_start: 0.7366 (pmm) cc_final: 0.6970 (mmt) REVERT: B 101 GLU cc_start: 0.7954 (mp0) cc_final: 0.7627 (mm-30) REVERT: B 142 LYS cc_start: 0.8193 (mttm) cc_final: 0.7968 (mptt) REVERT: W 78 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: W 103 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7310 (tm-30) REVERT: W 110 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8254 (tttm) REVERT: W 125 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: K 78 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: K 142 LYS cc_start: 0.8118 (mptt) cc_final: 0.7816 (mptt) REVERT: N 101 GLU cc_start: 0.7903 (mp0) cc_final: 0.7477 (mm-30) REVERT: H 78 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: H 110 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8223 (tttm) REVERT: L 49 GLU cc_start: 0.8510 (tt0) cc_final: 0.8272 (tt0) REVERT: L 78 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: L 110 LYS cc_start: 0.8962 (tttm) cc_final: 0.8700 (tttm) REVERT: M 101 GLU cc_start: 0.7934 (mp0) cc_final: 0.7494 (mm-30) REVERT: Q 49 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: Q 87 MET cc_start: 0.7339 (pmm) cc_final: 0.6921 (mmt) REVERT: Q 92 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: Q 101 GLU cc_start: 0.7881 (mp0) cc_final: 0.7621 (mm-30) REVERT: Q 142 LYS cc_start: 0.8155 (mttm) cc_final: 0.7945 (mptt) REVERT: J 101 GLU cc_start: 0.7922 (mp0) cc_final: 0.7465 (mm-30) REVERT: J 102 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: G 87 MET cc_start: 0.7334 (pmm) cc_final: 0.6956 (mmt) REVERT: G 101 GLU cc_start: 0.7942 (mp0) cc_final: 0.7634 (mm-30) REVERT: G 142 LYS cc_start: 0.8191 (mttm) cc_final: 0.7986 (mptt) REVERT: S 78 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: S 103 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7311 (tm-30) REVERT: S 110 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8242 (tttm) REVERT: V 78 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: V 110 LYS cc_start: 0.8947 (tttm) cc_final: 0.8681 (tttm) outliers start: 67 outliers final: 37 residues processed: 601 average time/residue: 1.5924 time to fit residues: 1062.8268 Evaluate side-chains 619 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 548 time to evaluate : 2.502 ------------------------------------------------------------------------------- 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 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 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 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 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 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 125 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain 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: 6.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.132374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105540 restraints weight = 23470.527| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.25 r_work: 0.3062 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.7857 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= 0.142 Angle : 0.622 8.885 29304 Z= 0.311 Chirality : 0.053 0.146 3480 Planarity : 0.004 0.030 3720 Dihedral : 4.063 13.230 2880 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.42 % Allowed : 26.12 % Favored : 70.46 % 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: 3.09 (0.15), residues: 1392 loop : -0.18 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE N 124 TYR 0.010 0.002 TYR F 106 ARG 0.001 0.000 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 945) hydrogen bonds : angle 3.84356 ( 2331) covalent geometry : bond 0.00345 (21720) covalent geometry : angle 0.62185 (29304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26180.43 seconds wall clock time: 447 minutes 49.11 seconds (26869.11 seconds total)