Starting phenix.real_space_refine on Sun Sep 29 02:54:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/09_2024/8wp9_37713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/09_2024/8wp9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/09_2024/8wp9_37713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/09_2024/8wp9_37713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/09_2024/8wp9_37713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/09_2024/8wp9_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-5461/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: 6.83, per 1000 atoms: 0.32 Number of scatterers: 21432 At special positions: 0 Unit cell: (132.581, 132.581, 132.581, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 4176 8.00 N 3528 7.00 C 13680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 2.7 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: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE A 140 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA P 120 " --> pdb=" O GLU P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE P 140 " --> pdb=" O GLU P 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 66 No H-bonds generated for 'chain 'T' and resid 64 through 66' Processing helix chain 'T' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA T 120 " --> pdb=" O GLU T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE T 140 " --> pdb=" O GLU T 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 66 No H-bonds generated for 'chain 'U' and resid 64 through 66' Processing helix chain 'U' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA U 120 " --> pdb=" O GLU U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE U 140 " --> pdb=" O GLU U 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE E 140 " --> pdb=" O GLU E 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA I 120 " --> pdb=" O GLU I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE I 140 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA X 120 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE X 140 " --> pdb=" O GLU X 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA D 120 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE D 140 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA F 120 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE F 140 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA R 120 " --> pdb=" O GLU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE R 140 " --> pdb=" O GLU R 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing helix chain 'O' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA O 120 " --> pdb=" O GLU O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE O 140 " --> pdb=" O GLU O 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA C 120 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE C 140 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE B 140 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 66 No H-bonds generated for 'chain 'W' and resid 64 through 66' Processing helix chain 'W' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA W 120 " --> pdb=" O GLU W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE W 140 " --> pdb=" O GLU W 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA K 120 " --> pdb=" O GLU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE K 140 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA N 120 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE N 140 " --> pdb=" O GLU N 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA H 120 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 66 No H-bonds generated for 'chain 'L' and resid 64 through 66' Processing helix chain 'L' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA L 120 " --> pdb=" O GLU L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE L 140 " --> pdb=" O GLU L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 66 No H-bonds generated for 'chain 'M' and resid 64 through 66' Processing helix chain 'M' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA M 120 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE M 140 " --> pdb=" O GLU M 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 66 No H-bonds generated for 'chain 'Q' and resid 64 through 66' Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA Q 120 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE Q 140 " --> pdb=" O GLU Q 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA J 120 " --> pdb=" O GLU J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE J 140 " --> pdb=" O GLU J 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA G 120 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE G 140 " --> pdb=" O GLU G 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA S 120 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE S 140 " --> pdb=" O GLU S 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 66 No H-bonds generated for 'chain 'V' and resid 64 through 66' Processing helix chain 'V' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA V 120 " --> pdb=" O GLU V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE V 140 " --> pdb=" O GLU V 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 146 through 147 removed outlier: 7.786A pdb=" N ALA A 122 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 96 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU A 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE C 94 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 5.633A pdb=" N ILE A 94 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU C 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 96 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA C 122 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.944A pdb=" N PHE B 124 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 96 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU B 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE D 94 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 36 through 40 Processing sheet with id=AA7, first strand: chain 'P' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR O 96 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU P 49 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE O 94 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE P 94 " --> pdb=" O GLU O 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU O 49 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR P 96 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AB1, first strand: chain 'P' and resid 146 through 147 removed outlier: 3.829A pdb=" N PHE G 124 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR H 96 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE H 94 " --> pdb=" O GLU G 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 36 through 40 Processing sheet with id=AB3, first strand: chain 'R' and resid 93 through 97 removed outlier: 5.617A pdb=" N ILE R 94 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU T 49 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 96 " --> pdb=" O ILE T 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA T 122 " --> pdb=" O GLU K 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 93 through 97 removed outlier: 5.526A pdb=" N ILE T 94 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU R 49 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR T 96 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 142 through 143 Processing sheet with id=AB6, first strand: chain 'T' and resid 146 through 147 removed outlier: 4.072A pdb=" N PHE X 124 " --> pdb=" O GLU T 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR W 96 " --> pdb=" O ILE X 47 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU X 49 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE W 94 " --> pdb=" O GLU X 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 36 through 40 Processing sheet with id=AB8, first strand: chain 'F' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE F 94 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU U 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 96 " --> pdb=" O ILE U 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA U 122 " --> pdb=" O GLU V 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE U 94 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 49 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR U 96 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA F 122 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 142 through 143 Processing sheet with id=AC2, first strand: chain 'U' and resid 146 through 147 removed outlier: 3.712A pdb=" N PHE Q 124 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR S 96 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU Q 49 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE S 94 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 147 removed outlier: 7.830A pdb=" N ALA E 122 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR N 96 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU E 49 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE N 94 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE E 94 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU N 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR E 96 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 36 through 40 Processing sheet with id=AC7, first strand: chain 'I' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR K 96 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU I 49 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE K 94 " --> pdb=" O GLU I 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE I 94 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU K 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR I 96 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE K 124 " --> pdb=" O GLU O 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 142 through 143 Processing sheet with id=AD1, first strand: chain 'I' and resid 146 through 147 removed outlier: 3.760A pdb=" N PHE J 124 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR L 96 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU J 49 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE L 94 " --> pdb=" O GLU J 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 93 through 97 removed outlier: 5.567A pdb=" N ILE X 94 " --> pdb=" O GLU W 49 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU W 49 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR X 96 " --> pdb=" O ILE W 47 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA W 122 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 142 through 143 Processing sheet with id=AD4, first strand: chain 'D' and resid 36 through 40 Processing sheet with id=AD5, first strand: chain 'B' and resid 93 through 97 removed outlier: 5.750A pdb=" N ILE B 94 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU D 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 96 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA D 122 " --> pdb=" O GLU S 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AD7, first strand: chain 'F' and resid 36 through 40 Processing sheet with id=AD8, first strand: chain 'R' and resid 36 through 40 Processing sheet with id=AD9, first strand: chain 'R' and resid 142 through 143 Processing sheet with id=AE1, first strand: chain 'R' and resid 146 through 147 removed outlier: 4.058A pdb=" N PHE V 124 " --> pdb=" O GLU R 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 96 " --> pdb=" O ILE V 47 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU V 49 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE M 94 " --> pdb=" O GLU V 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 40 Processing sheet with id=AE4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE5, first strand: chain 'W' and resid 36 through 40 Processing sheet with id=AE6, first strand: chain 'W' and resid 142 through 143 Processing sheet with id=AE7, first strand: chain 'N' and resid 36 through 40 Processing sheet with id=AE8, first strand: chain 'N' and resid 142 through 143 Processing sheet with id=AE9, first strand: chain 'N' and resid 146 through 147 removed outlier: 3.723A pdb=" N PHE M 124 " --> pdb=" O GLU N 147 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR V 96 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU M 49 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE V 94 " --> pdb=" O GLU M 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR G 96 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE G 94 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.635A pdb=" N TYR J 96 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU L 49 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE J 94 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 93 through 97 removed outlier: 5.581A pdb=" N ILE Q 94 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU S 49 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 5.64 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' 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: 8.050 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: 0.000 Extract box with map and model: 0.990 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 44.180 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 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:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.920 ------------------------------------------------------------------------------- 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= 0.350 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 *********************** 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 fitting. rotamer outliers: 24 poor density : 807 time to evaluate : 2.551 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: 1.6418 time to fit residues: 1491.5659 Evaluate side-chains 475 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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= 0.280 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 *********************** 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 fitting. rotamer outliers: 112 poor density : 647 time to evaluate : 2.532 Fit side-chains REVERT: A 93 ARG cc_start: 0.8277 (pmt170) cc_final: 0.7937 (pmt170) REVERT: A 102 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: E 49 GLU cc_start: 0.7802 (tt0) cc_final: 0.7563 (tt0) REVERT: E 78 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: E 102 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: E 104 GLU cc_start: 0.7336 (tp30) cc_final: 0.7092 (mm-30) REVERT: I 49 GLU cc_start: 0.7776 (tt0) cc_final: 0.7572 (tt0) REVERT: I 103 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: X 92 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: D 36 GLN cc_start: 0.8033 (mt0) cc_final: 0.7816 (tt0) REVERT: D 78 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: F 78 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: F 118 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: R 78 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: R 118 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: O 78 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: O 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: C 78 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: C 118 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: K 49 GLU cc_start: 0.7812 (tt0) cc_final: 0.7579 (tt0) REVERT: K 78 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: K 102 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: K 104 GLU cc_start: 0.7335 (tp30) cc_final: 0.7085 (mm-30) REVERT: N 103 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: L 78 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: L 104 GLU cc_start: 0.7350 (tp30) cc_final: 0.7108 (mm-30) REVERT: M 49 GLU cc_start: 0.7809 (tt0) cc_final: 0.7594 (tt0) REVERT: Q 92 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: V 78 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7831 (tm-30) outliers start: 112 outliers final: 16 residues processed: 717 average time/residue: 1.6729 time to fit residues: 1318.3352 Evaluate side-chains 575 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 539 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 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 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 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU 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 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 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 133 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.7394 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= 0.202 Angle : 0.605 8.290 29304 Z= 0.306 Chirality : 0.053 0.144 3480 Planarity : 0.004 0.027 3720 Dihedral : 4.169 13.912 2880 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.08 % Allowed : 21.33 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.19 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.14 (0.15), residues: 1392 loop : -0.60 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 59 HIS 0.006 0.001 HIS G 53 PHE 0.005 0.001 PHE V 124 TYR 0.011 0.002 TYR I 106 ARG 0.002 0.000 ARG A 93 *********************** 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 673 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 575 time to evaluate : 2.811 Fit side-chains REVERT: A 102 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: P 102 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: P 103 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: U 102 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: U 103 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: E 78 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: E 102 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: E 104 GLU cc_start: 0.7393 (tp30) cc_final: 0.7066 (mm-30) REVERT: D 91 SER cc_start: 0.5817 (OUTLIER) cc_final: 0.5530 (t) REVERT: F 78 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: F 118 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: R 78 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: R 118 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: O 78 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: O 118 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: C 78 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: C 110 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8687 (tttm) REVERT: C 118 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: W 78 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: K 78 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: K 102 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: K 104 GLU cc_start: 0.7387 (tp30) cc_final: 0.7061 (mm-30) REVERT: N 49 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: H 78 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: H 91 SER cc_start: 0.6018 (OUTLIER) cc_final: 0.5764 (t) REVERT: L 78 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: L 102 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: L 106 TYR cc_start: 0.8464 (p90) cc_final: 0.8255 (p90) REVERT: M 110 LYS cc_start: 0.8855 (tttm) cc_final: 0.8620 (tttm) REVERT: J 49 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: J 78 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: J 102 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: S 78 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: S 91 SER cc_start: 0.6019 (OUTLIER) cc_final: 0.5771 (t) REVERT: V 78 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7796 (tm-30) outliers start: 98 outliers final: 33 residues processed: 636 average time/residue: 1.5884 time to fit residues: 1116.2530 Evaluate side-chains 610 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 547 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 102 GLU Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 102 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 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 118 GLU Chi-restraints excluded: chain O residue 78 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 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 102 GLU 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 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 91 SER Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.7668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 21720 Z= 0.368 Angle : 0.734 9.279 29304 Z= 0.371 Chirality : 0.055 0.152 3480 Planarity : 0.005 0.042 3720 Dihedral : 4.636 14.516 2880 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.75 % Allowed : 21.25 % Favored : 74.00 % 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: 2.11 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.11 (0.15), residues: 1392 loop : -0.68 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.008 0.002 TYR V 106 ARG 0.003 0.001 ARG H 93 *********************** 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 688 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 574 time to evaluate : 2.797 Fit side-chains REVERT: A 78 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: A 103 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: P 78 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: T 78 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: U 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: E 102 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: E 104 GLU cc_start: 0.7420 (tp30) cc_final: 0.7204 (mm-30) REVERT: I 102 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: D 78 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: D 91 SER cc_start: 0.5830 (OUTLIER) cc_final: 0.5602 (t) REVERT: F 78 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: F 118 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: R 78 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: R 118 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: O 78 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: O 118 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: C 78 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: C 110 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8690 (tttm) REVERT: C 118 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: W 78 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: W 91 SER cc_start: 0.5733 (OUTLIER) cc_final: 0.5498 (t) REVERT: K 102 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: K 104 GLU cc_start: 0.7415 (tp30) cc_final: 0.7198 (mm-30) REVERT: N 102 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: H 78 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: H 91 SER cc_start: 0.5836 (OUTLIER) cc_final: 0.5598 (t) REVERT: L 78 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: J 78 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: S 78 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: V 78 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7845 (tm-30) outliers start: 114 outliers final: 50 residues processed: 653 average time/residue: 1.5907 time to fit residues: 1149.2840 Evaluate side-chains 633 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 556 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 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 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain 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 X residue 139 SER Chi-restraints excluded: chain D residue 40 LYS 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 F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 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 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 40 LYS 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 K residue 46 SER 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 40 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain 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 116 LYS 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 G residue 102 GLU Chi-restraints excluded: chain S residue 40 LYS Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.7702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 21720 Z= 0.317 Angle : 0.691 9.076 29304 Z= 0.348 Chirality : 0.054 0.147 3480 Planarity : 0.004 0.036 3720 Dihedral : 4.500 13.876 2880 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.50 % Allowed : 22.75 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.66 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.007 0.002 TYR X 106 ARG 0.002 0.001 ARG E 80 *********************** 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 676 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 568 time to evaluate : 2.808 Fit side-chains REVERT: A 78 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: P 78 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: P 103 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: T 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: U 78 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: U 103 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: E 78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: E 102 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: I 102 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: D 78 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: D 91 SER cc_start: 0.5756 (OUTLIER) cc_final: 0.5552 (t) REVERT: F 78 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: F 118 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: R 78 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: R 118 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: O 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: O 118 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: C 78 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: C 110 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8685 (tttm) REVERT: C 118 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: B 49 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: W 78 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: W 91 SER cc_start: 0.5736 (OUTLIER) cc_final: 0.5510 (t) REVERT: K 78 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: K 102 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: N 102 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: H 78 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: H 91 SER cc_start: 0.5816 (OUTLIER) cc_final: 0.5600 (t) REVERT: L 78 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: J 78 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: J 102 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: S 78 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: V 78 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7857 (tm-30) outliers start: 108 outliers final: 58 residues processed: 643 average time/residue: 1.5259 time to fit residues: 1089.3178 Evaluate side-chains 652 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 562 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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 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 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 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 X residue 139 SER Chi-restraints excluded: chain D residue 40 LYS 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 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain O residue 145 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 40 LYS 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 K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain 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 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 J residue 121 SER Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 40 LYS Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain 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 85 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 0.0770 chunk 62 optimal weight: 6.9990 chunk 255 optimal weight: 0.3980 chunk 212 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.7728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21720 Z= 0.123 Angle : 0.513 7.763 29304 Z= 0.258 Chirality : 0.051 0.142 3480 Planarity : 0.003 0.023 3720 Dihedral : 3.682 12.521 2880 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.12 % Allowed : 25.00 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.18 (0.15), residues: 1392 loop : -0.23 (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 0.009 0.001 TYR V 106 ARG 0.001 0.000 ARG X 93 *********************** 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 650 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 575 time to evaluate : 2.850 Fit side-chains REVERT: A 49 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: A 78 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: P 78 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: P 103 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: T 78 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: U 78 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: U 103 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: E 78 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: E 110 LYS cc_start: 0.8849 (tttm) cc_final: 0.8611 (tttm) REVERT: D 78 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: F 118 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: R 118 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: O 118 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: C 118 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: W 78 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: K 78 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: K 110 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8474 (tttm) REVERT: H 78 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: L 110 LYS cc_start: 0.8853 (tttm) cc_final: 0.8612 (tttm) REVERT: M 102 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: J 102 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: S 78 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: V 110 LYS cc_start: 0.8859 (tttm) cc_final: 0.8618 (tttm) outliers start: 75 outliers final: 38 residues processed: 624 average time/residue: 1.5011 time to fit residues: 1040.9010 Evaluate side-chains 608 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 551 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain 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 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 145 ASN 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 118 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 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 H residue 145 ASN Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 21720 Z= 0.296 Angle : 0.668 8.827 29304 Z= 0.337 Chirality : 0.054 0.147 3480 Planarity : 0.004 0.037 3720 Dihedral : 4.285 13.497 2880 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.42 % Allowed : 24.92 % Favored : 71.67 % 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: 2.26 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.11 (0.15), residues: 1392 loop : -0.43 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.010 0.002 TYR U 106 ARG 0.002 0.001 ARG H 93 *********************** 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 649 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 567 time to evaluate : 2.889 Fit side-chains REVERT: A 78 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: P 78 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: P 103 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: T 78 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: U 78 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: U 103 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: E 78 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: E 102 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: I 102 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: D 78 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: F 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: F 118 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: R 78 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: R 118 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: O 78 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: O 118 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: C 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: C 118 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: B 142 LYS cc_start: 0.8291 (mptt) cc_final: 0.7913 (mptt) REVERT: W 78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: W 102 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: K 78 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: K 102 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: N 102 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: H 78 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: H 102 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: L 78 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: M 102 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: J 78 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: J 102 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: S 78 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: V 78 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7761 (tm-30) outliers start: 82 outliers final: 37 residues processed: 628 average time/residue: 1.6084 time to fit residues: 1116.1760 Evaluate side-chains 632 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 564 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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 P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain 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 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 118 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain O residue 145 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 102 GLU 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 78 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain 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 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 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.7783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21720 Z= 0.178 Angle : 0.573 8.260 29304 Z= 0.288 Chirality : 0.052 0.145 3480 Planarity : 0.003 0.025 3720 Dihedral : 3.921 13.005 2880 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.38 % Allowed : 25.25 % Favored : 71.38 % 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: 2.35 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.28 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 59 HIS 0.002 0.001 HIS T 53 PHE 0.005 0.001 PHE M 124 TYR 0.006 0.001 TYR G 106 ARG 0.001 0.000 ARG E 80 *********************** 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 639 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 558 time to evaluate : 2.627 Fit side-chains REVERT: A 78 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: P 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: P 103 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: T 78 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: U 78 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: U 103 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: E 78 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: E 102 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: E 110 LYS cc_start: 0.8850 (tttm) cc_final: 0.8603 (tttm) REVERT: I 102 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: X 49 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: D 78 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: F 78 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: F 118 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: R 78 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: R 118 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: O 78 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: O 118 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: C 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: C 118 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: W 78 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: K 78 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: K 102 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: N 102 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: H 78 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: L 110 LYS cc_start: 0.8860 (tttm) cc_final: 0.8614 (tttm) REVERT: M 102 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: J 78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: J 102 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: S 78 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: V 110 LYS cc_start: 0.8857 (tttm) cc_final: 0.8609 (tttm) outliers start: 81 outliers final: 44 residues processed: 616 average time/residue: 1.5780 time to fit residues: 1078.6388 Evaluate side-chains 624 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 552 time to evaluate : 2.661 ------------------------------------------------------------------------------- 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 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 49 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 78 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 118 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain O residue 145 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 145 ASN 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 78 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 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 243 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.7723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21720 Z= 0.161 Angle : 0.557 7.969 29304 Z= 0.279 Chirality : 0.052 0.143 3480 Planarity : 0.003 0.024 3720 Dihedral : 3.801 12.804 2880 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.92 % Allowed : 26.33 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.19 (0.17), 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 0.005 0.001 PHE M 124 TYR 0.012 0.002 TYR P 106 ARG 0.001 0.000 ARG V 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 547 time to evaluate : 2.716 Fit side-chains REVERT: A 49 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 78 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: P 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: P 103 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: T 78 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: U 78 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: U 103 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: E 78 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: E 110 LYS cc_start: 0.8844 (tttm) cc_final: 0.8600 (tttm) REVERT: I 102 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: D 78 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: F 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: F 118 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: R 78 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: R 118 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: O 78 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: O 118 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: C 78 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: C 118 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: W 78 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: K 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: N 102 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: H 78 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: H 102 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: L 78 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: L 110 LYS cc_start: 0.8854 (tttm) cc_final: 0.8612 (tttm) REVERT: M 102 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: J 78 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: J 102 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: S 78 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: V 78 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: V 110 LYS cc_start: 0.8852 (tttm) cc_final: 0.8610 (tttm) outliers start: 70 outliers final: 41 residues processed: 604 average time/residue: 1.5480 time to fit residues: 1035.0092 Evaluate side-chains 612 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 542 time to evaluate : 2.527 ------------------------------------------------------------------------------- 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 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 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 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 78 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 118 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain O residue 145 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 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 145 ASN Chi-restraints excluded: chain M residue 102 GLU 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 J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 242 optimal weight: 0.5980 chunk 209 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.7816 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= 0.175 Angle : 0.576 8.011 29304 Z= 0.288 Chirality : 0.052 0.145 3480 Planarity : 0.003 0.025 3720 Dihedral : 3.853 12.857 2880 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.17 % Allowed : 26.88 % Favored : 69.96 % 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: 2.39 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.08 (0.15), residues: 1392 loop : -0.19 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE M 124 TYR 0.005 0.001 TYR B 106 ARG 0.001 0.000 ARG K 80 ********************** 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 618 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 542 time to evaluate : 3.105 Fit side-chains REVERT: A 49 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: A 78 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: P 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: P 103 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: U 78 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: U 103 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: E 78 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: E 110 LYS cc_start: 0.8848 (tttm) cc_final: 0.8601 (tttm) REVERT: I 102 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: X 49 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: X 142 LYS cc_start: 0.8113 (mptt) cc_final: 0.7840 (mptt) REVERT: D 78 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: F 78 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: F 118 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: R 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: R 118 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: O 78 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: O 118 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: C 78 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: C 118 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: W 78 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: W 102 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: K 78 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: N 102 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: N 142 LYS cc_start: 0.8143 (mptt) cc_final: 0.7872 (mptt) REVERT: H 78 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: H 102 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: L 78 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: L 110 LYS cc_start: 0.8853 (tttm) cc_final: 0.8608 (tttm) REVERT: M 102 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: J 78 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: J 102 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: S 78 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: S 102 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: V 78 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: V 110 LYS cc_start: 0.8857 (tttm) cc_final: 0.8610 (tttm) outliers start: 76 outliers final: 47 residues processed: 604 average time/residue: 1.5694 time to fit residues: 1048.8043 Evaluate side-chains 618 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 540 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 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 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 49 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 40 LYS Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain O residue 145 ASN Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 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 145 ASN Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 145 ASN 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 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 Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 209 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.135990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109125 restraints weight = 23243.788| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.23 r_work: 0.3101 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 21720 Z= 0.183 Angle : 0.586 8.168 29304 Z= 0.293 Chirality : 0.052 0.146 3480 Planarity : 0.003 0.025 3720 Dihedral : 3.876 12.896 2880 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.33 % Allowed : 26.88 % Favored : 69.79 % 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: 2.38 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.07 (0.15), residues: 1392 loop : -0.21 (0.17), 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 0.005 0.001 PHE M 124 TYR 0.009 0.002 TYR R 106 ARG 0.001 0.000 ARG K 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15320.97 seconds wall clock time: 264 minutes 47.08 seconds (15887.08 seconds total)